The invention provides a machining system and a machining method thereof. The machining system comprises an automatic feeding frame, a transmission device, a cutting saw, a transport device, a machining device and a controller. The automatic feeding frame of the machining system is used for transporting boards to be machined to the transmission device, the transmission device is used for transporting the boards to a board cutting position of the cutting saw, the cutting saw is used for cutting the boards, the transport device is used for transporting the cut boards to a board machining position of the machining device, the machining device is used for machining reference surfaces of the boards, and starting, stopping and shifting of the automatic feeding frame, the transmission device, the cutting saw, the transport device and the machining device of the whole machining system are controlled by a controller. The whole action process needs no manual operation, machining operation of the whole machining procedure can be completed rapidly and accurately, and careless mistakes can be avoided.