The invention discloses a fluorescent molecular imaging system based on an LED light source and an imaging method thereof. The fluorescent molecular imaging system based on the LED light source comprises a light source device, an animal bed, an imaging device and a computer image processing system, wherein the light source device comprises the light source, a light source frame, a switch set, an exciting light filter set and lenses. LEDs are adopted in the light source, the light source comprises multiple sets of LED arrays of different light-emitting wave lengths, and each set of the LED array is connected to the switch set. According to the fluorescent molecular imaging system based on the LED light source and the imaging method thereof, the multiple sets of the LED arrays of different light-emitting lengths are adopted in the light source, the manufacturing technology is simple, price is low, and the LED arrays of different wave lengths can be switched easily according to needs to achieve the excitation of different fluorescent substances. It is firstly proposed that the LEDs serve as the exciting light source of the transmission-type fluorescent molecular imaging system and the exciting light source of a fluorescent molecular tomography system, the imaging system is simple in structure, optical fibers are not needed for transmitting exciting light, and therefore fluorescent molecular tomography can be carried out more efficiently.