The invention discloses a multi-color super-resolution imaging system applied to a 4pi microscopic structure. The multi-color super-resolution imaging system comprises a light source module, a sampletable, an upper microscope lens, a lower microscope lens, a first quarter-wave plate, a second quarter-wave plate, a first dichroscope, a second dichroscope, a first light path reflex matching unit, asecond light path reflex matching unit, a first deformable mirror, a second deformable mirror, a first Babinet's compensator, a second Babinet's compensator, a beam splitter cube, a third light pathreflex matching unit, a fourth light path reflex matching unit, a polarization beam splitter cube, an eleventh reflector, a twelfth reflector, a ninth lens, a tenth lens, a rectangular prism, a thirddichroscope, an eleventh lens, a twelfth lens, a first imaging device and a second imaging device. According to the system, the unimolecule positioning technology and crosstalk among different fluorescent molecules are utilized, and in combination with the 4pi microscopic technology, multi-color three-dimensional super-resolution imaging of whole cells is achieved.