Morris grew up in Texas in the 1920s and 1930s. He graduated from Rice University with a bachelor's degree in civil engineering in 1939. He married Mary Louise on January 24, 1940, and they later had six children. After his graduation in 1939, and through 1942, he was a hydraulic engineer working with the International Boundary and Water Commission. He returned to Rice, teaching civil engineering from 1942 until 1946. In 1946 he wrote a short book entitled That You Might Believe (1946), in which he made an effort to attack evolution. From 1946 through 1951, he studied at the University of Minnesota, where he was awarded a master's degree in hydraulics (1948) and a Ph.D. in hydraulic engineering (1950).

In 1951 he became a professor and chair of civil engineering at the University of Louisiana at Lafayette. He then served as a professor of applied science at Southern Illinois University, 1956...1957, and subsequently as professor of hydraulic engineering and in civil engineering at the Virginia Polytechnic Institute and State University (Virginia Tech), again serving as the department chair.

In 1963 Morris and nine others founded the Creation Research Society. After a dispute with the administration of the university , Morris resigned from his position at Virginia Tech in 1969. In 1970, he co-founded the Christian Heritage College in Santee, California which spawned Institute for Creation Research (ICR) in 1972. His son, John D. Morris, took over the presidency of ICR when his father retired.

On February 1, 2006, Morris suffered a minor stroke and was hospitalized. Morris was moved from the hospital to a rehabilitation facility near his son's home (and ICR) in Santee, California where he died.

In 1961, Morris and John C. Whitcomb wrote The Genesis Flood, which advocated creationism and flood geology. In it he cited an influence by George McCready Price, a Seventh-day Adventist schoolteacher and defender of creationism in the early 20th century. This work sold more than 200,000 copies worldwide, despite being a non-fiction book of little popular interest.

While the greater bulk of his published writings address creation science and evolution themes, he had also written Many Infallible Proofs, and The Bible Has The Answer, which are both works of general Christian apologetics.

Morris received criticism from the scientific community for his philosophy of science, and his representation of evolution as a complete religious system has been called a straw man. In particular, Massimo Pigliucci criticized Morris' omission of material that interferes with his "mission" and "beliefs". Pigliucci also criticized Morris' intrepretation of thermodynamics. Morris' position had also been the subject of debate among Evangelical scholars of the Old Testament and among Evangelicals working in various fields of science. Morris also strongly defended the use of the King James Bible.

In Evolution & the Modern Christian (1967), Morris hoped to "open the minds and hearts of young people to the true Biblical cosmology." T.E. Fenton, Professor of Agronomy at Iowa State University, wrote "scientific value of the book is nil; the author selectively chooses the areas of science that he accepts and rejects other areas of accepted science".

Morris wrote in The Remarkable Birth of Planet Earth (1972) that the craters of the moon were caused by a cosmic battle between the forces of Satan and the armies of the archangel Michael. David Vogel, Professor of Biology at Creighton University, reviewed the book explaining "his theology is shallow; his exegesis is maddening; his science is wrong; and he tops it off by offending millions of Bible-believing Christians who also accept evolution".

His book Scientific Creationism (1974 and 1984), according to Herman Kirkpatrick, "is not very convincing evidence to support the recent creation of the earth". Thomas Wheeler, Professor of biochemistry at University of Louisville, reviewed the second edition and concluded, "Scientific Creationism cannot be recommended for use in public school classes, or indeed anyone interested in learning science". Wheeler cited Morris misunderstanding of science, appeals to religious prejudice, misrepresentation of scientific knowledge, omission of opposing science, double standards in evidence, "absurd conclusions," inappropriate and misidentified sources, attacks on scientists, using discredited arguments, and "silly calculations".

Morris' work with John C. Whitcomb, The Genesis Flood, has been criticized for taking quotes out of context and misquoting sources. For example, in one instance, a source which read "the sea which vanished so many million years ago" was quoted as "the sea which vanished so many years ago." Geologist John G. Solum has criticized the work for being inaccurate. Solum noted "Whitcomb and Morris are mistaken about the nature of the rocks associated with thrust faults. Their claim about fossils is based on a YEC misunderstanding of how rocks are dated relative to each other, and how the geologic column was constructed." In fact Solum noted, "Morris' explanation of relative dating is not 'somewhat oversimplified' it is entirely incorrect."

In The Long War Against God: The History and Impact of the Creation/Evolution Conflict (1989) Morris wrote that "the denial of God - rejecting the reality of supernatural creation and the creator's soverign rule of the world - has always been the root cause of every human problem." Morris was criticized by Randy Moore, of University of Minnesota, for writing in the book that "evolutionism" is satanic and responsible for racism, abortion, and a decline in morality.