A signal control system for a fan motor comprises an input end, a load driving unit, a first signal conversion unit, a second signal conversion unit, and an amplifying driving unit. A rotation speed signal is transmitted from the input end to the load driving unit. The first and the second signal conversion units are electrically connected to the load driving unit and receive the rotation speed signal. The amplifying driving unit is electrically connected to the first and the second signal conversion units to generate an operation signal. Thus, the received rotation speed signal is converted to the operation signal through the signal control system for the fan motor, achieving the effects of cost reduction, simplification, and convenience.