The invention discloses a multi-mode little animal molecular image imaging device and an imaging method thereof. The device comprises an X-ray computer tomography (CT) system, a positron emission tomography (PET) system, a single photon emission computed tomography (SPECT) system, a fluorescence molecular tomography (FMT) system, a rotating rack system, a little animal bed system, a data acquisition system and a computer, various imaging systems are sampled and stored by the data acquisition system through a data line into the computer, and various imaging systems share one little animal bed system and the same inspection shaft. According to the multi-mode little animal molecular image imaging device and the imaging method, various imaging systems share one little animal bed system and the same inspection shaft, an installing fusion molecular medicine image of four modes of X-ray CT, PET, SPECT and FMT can achieve complementary advantages of different image devices, and the obtained image result is accurate and reliable.