He was a prominent Bourbon Democrat, taking a conservative position on political, economic, and social issues, and opposing agrarianism.

In his junior year he attempted to launch a new periodical, the Peninsular Quarterly and University Magazine, which proved short-lived.

He was an active member of the Chi Psi fraternity, and opposed an attempt by the faculty to discourage such secret societies.

[6] In May 1854, six weeks before Morton was due to graduate, the university's Board of Regents dismissed the head of the medical department, Dr. J. Adams Allen, a popular faculty member.

The following day, Morton was expelled from the university, ostensibly for excessive absences and for general inattention to his duties as a student.

The university president, Henry Philip Tappan, released a version of his statement from which the conditionals had been removed, making it a straightforward admission of fault.

Morton wrote a letter to the Detroit Free Press in which he retracted his original statement, declaring that he had not "...meanly petitioned, implored and besought the Faculty for mercy, for... the Latin-scratched integument of a dead sheep."

Morton used his positions as newspaperman and Secretary of the territory to oppose the so-called "Black Republicans" in the legislature, often using racist arguments.

[9] During the Civil War he was a harsh critic of President Lincoln and was considered a racist, Southern-sympathizing, copperhead Democrat with questionable loyalty to the Union, although he supposedly opposed succession as well as abolition.

Morton contested the outcome, noting that the Governor issued the second certificate in secret, without the concurrence of the Board of Canvassers and without the proper seal.

He is credited with helping change that department into a coordinated service to farmers, and he supported Cleveland in setting up national forest reservations.

Today, Joy Morton's original 400-acre (1.6 km2) Thornhill Estate, which he acquired in 1910, has been transformed into a 1,700-acre (6.9 km2) living history museum of over 4,000 different types of trees, shrubs, and other woody plants.