It is the only university directly charged by the government to advance the cause of national unity and actively pursue integration through education.

From a one campus university in Marawi, MSU has grown to a multi-campus university of eight autonomous campuses: MSU-Main in Marawi, MSU-IIT in Iligan, MSU-TCTO in Tawi-Tawi, MSU-Naawan in Misamis Oriental, MSU-Maguindanao, MSU-General Santos, MSU-Sulu in Jolo, MSU Buug in Zamboanga Sibugay, and MSU-Bataraza in Palawan.

Baccalaureate courses were offered by the pioneering colleges: Liberal Arts, Education and Community Development to which four more were added in the subsequent school year 1964–65 – Agriculture, Fisheries, Business Administration and Engineering.

On January 10, 2001, three CHED supervised institutions — Lanao del Norte Agricultural College (LNAC), Lanao National College of Arts and Trades (LNCAT), and Maigo School of Arts and Trades (MSAT) — were integrated into the MSU System by virtue of CHED Order No.

Some students, faculty, and personnel were evacuated to nearby MSU-IIT in Iligan while others went home to their provinces during the ongoing conflict.

However, regular in-campus classes resumed in August of the same year after a successful Balik MSU: Somombak Tano sa Pantaw a Mareg campaign to allow faculty and students to return to the campus amidst the ongoing war with security being strictly monitored.

[14] Classes were temporarily suspended until further notice;[15] as a result, students, faculty, and personnel were repatriated to their home provinces following the incident.