The invention relates to a method for realizing flexible central fovea imaging based on a rotary biprism imaging system. The method comprises the steps of S1, constructing a rotary biprism imaging system; S2, constructing a fitness function, and defining a definition and calculation method of a fitness value; S3, determining a region of interest and the number of sub-images, and solving a prism rotation angle by using a particle swarm optimization algorithm; S4, sequentially adjusting the rotation angles of the prisms according to the result of the particle swarm optimization algorithm, and collecting images; S5, carrying out distortion correction on the collected images; S6, splicing the distorted and corrected images to obtain a large field of view; and S7, performing super-resolution reconstruction on the region of interest to further improve the resolution of the central fovea region. According to the invention, central fovea imaging with flexible adjustment of the region of interest can be realized, and acquisition of an overall large field of view is considered. Besides, central fovea imaging can be realized only by using the single rotary biprism imaging system, so that the complexity of equipment is greatly reduced, and the method has excellent practical value.