The invention discloses an automatic diode separating and carrying system and a separating and carrying method thereof. The system comprises a support plate, and a rectangular coordinate robot, a carrying mechanism and a separating mechanism which are disposed on the support plate. The separating mechanism comprises a support, a module fixing plate, a module and a jacking device. The jacking device comprises a first push-tooth plate, a second push-tooth plate, a first jacking air cylinder and a second jacking air cylinder, wherein the push teeth of the first push-tooth plate and the push teeth of the second push-tooth plate are staggered, and the piston rod of the first jacking air cylinder and the piston rod of the second jacking air cylinder penetrate the support plate and are respectively fixedly connected with the first push-tooth plate and the second push-tooth plate. The carrying mechanism carries a diode, the module fixing plate and the module which are jacked by the jacking device. The automatic diode separating and carrying system has the advantages that automatic 'separating' during diode machining is achieved, and the system is simple in structure, stable in operation, fast in separation, and high in positioning precision.