The college has a profound historical background and was developed based on the four majors of "Hydrographic Survey", "Ship Electric Automation", "Weapon Automation", and "Missile Launching System" in the Naval Engineering Department of the former Chinese People's Liberation Army Military Engineering Institute (referred to as "Harbin Military Industry"). In 1998, the Automation College was established by the combination of the Department of Automatic Control and the Missile Control Major and the System Engineering Research Office of Harbin Shipbuilding Engineering Institute. In 2020, the Intelligent Science and Engineering College was established.

The ship electric major created by the Naval Engineering Department of Harbin Military Industry was the first of its kind among higher education institutions in China. The ship electric major started enrolling students in 1955, and in 1960, the "Shipborne Missile Launching System" major was established within the Electrical Equipment Specialty. In 1970, based on the launching system major and the research group on reducing rolling fins, the "Ship Weapon Equipment Automatic Control" major with an automatic control nature for weapons and ship control was formed. In October 1975, the Ministry of the Sixth Machine-Building Industry decided to merge the 401 and 403 majors and change the name of the ship electric major to "Ship and Shipyard Electrical Automation" major. In February 1986, based on the document No. [1986] 59 of the China State Shipbuilding Corporation, the "Industrial Electrical Automation" undergraduate major was added. In July 1991, the Ministry of Education approved the establishment of 32 undergraduate majors in the Shipbuilding Institute, including industrial electrical automation and automatic control.

The college started enrolling master's degree students in 1965. In 1981, the State Council Academic Degrees Committee approved the granting of a master's degree in the "Gyro Navigation Equipment" major at Harbin Shipbuilding Institute, making it the first in the country. In 1990, the discipline of "Control Theory and Control Engineering" was granted a national second-level doctoral degree-granting discipline. In 1993, the discipline of "Navigation, Guidance, and Control" was granted a national second-level doctoral degree-granting discipline. In 1998, the discipline of "Control Science and Engineering" was granted a national first-level doctoral degree-granting discipline and a first-level discipline postdoctoral research mobile station. In 2001, the discipline of "Navigation, Guidance, and Control" was designated as a national key discipline. In 2011, the discipline of "Control Science and Engineering" was rated as excellent in the key discipline evaluation of Heilongjiang Province. In 2012, the discipline of "Control Science and Engineering" ranked 17th in the overall level of the third-round discipline evaluation of the Ministry of Education (with a percentile ranking of 20.5%).

The college has a glorious history in scientific research. The first set of shipborne inertial navigation systems (Nan Guandao), the first set of gyro single-axis stabilizers, the first set of rolling fins, and the first set of shipborne platform compasses were all born here. After the establishment of the Automation College, the college has successively developed the first set of shipborne integrated navigation systems in China, the first set of optical gyro navigation systems equipped by the Chinese Navy, the first set of embedded navigation and maneuvering training equipment for submarines, the first set of naval campaign maneuvering navigation systems, the first "dual-purpose" underwater mine detection and salvage vehicle, and the first independently developed set of rolling fins. It is the only unit in China with the capability to export rolling fins. The college has also developed the first set of dynamic positioning systems in China and established the fourth research and development base in the world and the only one in China that can produce dynamic positioning products.