The invention discloses a double-shaft photoelectric rotary table compound control system and a control method based on fuzzy decision. The control system comprises an integrated digital filtering, an estimation unit, a feed-forward control unit, a measuring unit, a change-over switch, a fuzzy-decision unit, a piping and instrument diagram (PID) controller, and a signal superposition unit. The double-shaft photoelectric rotary table position error e is compared with an error threshold K c set in advance, when e is less than K c, the fussy regulation is entered and regulation output controlled quantities delta kp, delta k and delta kd are obtained. PID control and regulation parameters kp, ki and kd are further obtained, and PID calculation is conducted. Otherwise, PID calculation is conducted by the utilization of the fixed regulation parameter set in advance and control signals outputted by PID are obtained. The effects of nonlinearity, time-varying characteristics, and model uncertainty on accuracy of the double-shaft photoelectric rotary table are effectively reduced. The problems of integral saturation and high frequency disturbance in the PID controller are solved, stochastic noise in the given stochastic signals is overcome, and long-term continuous stable work of the double-shaft photoelectric rotary table compound control system is ensured.