An auto focusing method based on simulated annealing algorithm is presented to recover the respective high resolution images for three different illumination colors， thus to recover the high resolution color image. Simulation modeling as well as the experiments on resolution target and biological slices all demonstrate that the high resolution color image can be recovered even for the microscopic system with serious chromatic aberration， which significantly relaxes the request for high quality microscope， thus expanding the application scope of the Fourier ptychographic microscopy.