In 1953，the predecessor of Harbin Engineering University, PLA Military Institute of Engineering founded. General Chen Geng was the first president.

In 1961, the Institute was identified as a national key university.

In 1966, PLA Military Institute was renamed as Harbin Engineering Institute and seceded from military academy.

In 1970, Harbin Institute of Shipbuilding Engineering was established at the original site of PLA Military Institute of Engineering.

In 1978, Harbin Institute of Shipbuilding Engineering was identified as a state key university by National Education Commission.

In April 1994, Harbin Institute of Shipbuilding Engineering was renamed Harbin Engineering University(HEU).

In 1996, the University became one of the first  universities of the national "211 Project".

In 2002, Ministry of Science and Technology and Ministry of Education approved the University to start the construction of "National University Science and Technology Park".

In 2003, the Graduate School of Harbin Engineering University was officially established, marking that Harbin Engineering University became one of 56 key universities with graduate schools.

In 2007， Harbin Engineering University was approved as one of the Chinese Government Scholarship institutions.

In 2008, the governing body of Harbin Engineering University changed to Ministry of Industry and Information Technology.

In 2010, Harbin Engineering University was approved for the national "Superior Subjects Platform".

In 2012，Harbin Engineering University and the South Ukrainian National Pedagogical University jointly established Confucius Institute.

In 2017, Harbin Engineering University was approved for the national "double first-class" plan for its distinctive advantages in "Naval Architecture, Ocean Development and Nuclear Power Application".