A control system, a mouse and a control method thereof are provided. The control system comprises a dongle and the mouse. The dongle is wiredly connected to a host and has a first light source for emitting a first light. The mouse is wirelessly connected to the dongle and has a transmitter, a second light source for emitting a second light, an optical sensor and a processor. The optical sensor senses the first light at a first time interval to generate a first sensing signal and then also, senses the second light at a second time interval to generate a second sensing signal. The processor generates a first control signal and a second control signal according to the first sensing signal and the second sensing signal, respectively, and transmits them to the dongle via the transmitter so that the host receives the first and second control signals via the dongle.