The invention provides a color computational holography aberration compensation system and method based on a varifocus lens. The system comprises a red laser device, a green laser device, a blue laser device, a shutter I, a shutter II, a shutter III, a filter I, a filter II, a filter III, a collimating lens I, a collimating lens II, a collimating lens III, a reflecting lens, a semi-transmission semi-reflecting lens I, a semi-transmission semi-reflecting lens II, a space light modulator, a computer, a driving panel, the varifocus lens, a receiving panel and a synchronous control circuit. The varifocus lens is used for replacing a solid lens commonly used in a color computational holography optics reappearing process, the varifocus performance of the varifocus lens is used, the focal lengths of the varifocus lens during reappearing of light with different colors are changed, so that R, G and B three-color reappearing image axial coinciding is achieved, accordingly, aberration compensation is achieved, the system can be effectively simplified, cost is lowered, and reappearing image quality is improved.