In September 1996, Wuhan Institute of Physics, CAS and Wuhan Institute of Mathematics, CAS were joined to be a new institute named Wuhan Institute of Physics and Mathematics, CAS.

In 1958, Wuhan Institute of Electronics, CAS was founded, which became Institute of Electronics of Southern-Central China in 1961 by combining with other twelve institutes in Southern-Central China. In 1962, the name was changed again by joining in Institute of Physics of Southern-Central China, and changed again in 1971 as Hubei Institute of Physics, CAS, and in 1978 as Wuhan Institute of Physics, CAS.

In 1956, Wuhan Research Department of Mathematics, CAS was founded, and then was expanded in 1959 to be Institute of Mathematics, Computing Technology and Automation, CAS. In 1961, the name was changed as Institute of Mathematics and Computing Technology, CAS after absorbing other institutes for computing technology and automation in Southern-Central China, In 1958, the department was moved to the No 7 institute of Navy belonging to the National Defence Commission for Science, Technology and Industry, and then transferred to the No 6 National Ministry of Machinery Industry.The name was changed again in 1979 to be Wuhan Institute of Mathematical Physics, CAS.

In 1986, the State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics was approved by National Planning Commission, and then examined by the government and finally founded in 1988.The Laboratory was involved in Knowledge Innovation Program in 1999. Since then, the laboratory has been built to be an international research base for NMR and atomic and molecular physics research, for academic exchange and for training specialists.

In November, 1999, Youth Laboratory of Ionospheric Physics and Youth Laboratory of Mathematical Physics were selected to be into the Knowledge Innovation (trial) Program, CAS.

In April 2001, Wuhan Research Center for Magnetic Resonance was founded by combining the Key State Laboratory of Magnetic Resonance and Atomic and Molecular Physics and the Second Clinic College, Wuhan University. The Center was approved in June 2008 as one of the thirteen National Centers for Huge Scientific Instruments.

In December 2001, WIPM was selected as a whole into the Knowledge Innovation (trial) Program, CAS. In March, 2003, Wuhan Center for Cold Atoms was founded by WIPM, CAS in joint with Shanghai Institute for Optics and Fine Mechanics, CAS.

In November 2003, Wuhan National Laboratory for Optics and Electronics was approved for foundation by National Ministry of Science and Technology of China. WIPM is one of the four preliminary units. Professor YE Chaohui, WIPM, was nominated to be the first Director of the Wuhan National Laboratory for Optics and Electronics.

In March 2006, Joint Laboratory of Mathematical Physics was founded by combining WIPM, University of Science and Technology of China, and the Academy of Mathematics and Systems Science, CAS.