Desalinating sea ice to obtain fresh water is a new way to solve the water shortage. Centrifugal desalination (CD) is an important method for desalination of sea ice, and it is of great significance to improve desalination efficiency. Microwave heating has a significant effect on improving salt-water separation efficiency, but the effect on centrifugal desalination is still unclear. In this paper, sea ice centrifugal desalination by microwave heating (CDBMH) was designed. The four factors of the particle size of ice, initial ice temperature, relative centrifugal force and centrifugation time were selected from the key parameters of centrifugal technology and sea ice material properties, and the impact of each factor on the salinity of the melted water, the desalination rate, and the water yield rate was explored. The results showed that with the decrease of the particle size of ice, the increase of initial ice temperature, relative centrifugal force and centrifugation time, the desalination rate showed an upward trend, while the water yield rate and the salinity of the melted water gradually decreased. As a result of the CDBMH process, the desalination rate was 93.3%, and the water yield rate was 72.4%, and the salinity of the melted water was 0.4 parts per thousand.