The invention relates to a method and system for correcting images shot in a stereoscopic mode. The method for correcting the images shot in the stereoscopic mode comprises the following steps that S1, the color deviation ratio of two camera modules used for stereoscopic shooting in a standard color temperature environment is acquired; S2, the color temperature of a used environment is measured, and the current color deviation ratio is determined; S3, two ways of images acquired by the two camera modules are corrected according to the current color deviation ratio. According to the method and system, the deviation of all ways of images on color and brightness can be adjusted dynamically in real time, the influence of the difference of an image sensor and environment light on imaging is removed, and the watching comfort level and the stereoscopic feeling can be obviously improved.