It is difficult to set up a precise model because of the inherent uncertainties of a photoelectric tracking system. The physical model of inherent characteristics was built for structural uncertainties of the photoelectric tracking system,and the transfer function of the system was obtained. On this basis,the sensitivity function matrix can be derived by first-order sensitivity function method,and the sensitivity curve and value can also be gotten by trajectory sensitivity method and perturbation method. The sensitivity track shows that the resistance of motor has the biggest influence on speed;the equivalent rotational inertia Jm of motor-transmission chain-load can also affect the speed;the inductance L of motor has minimal effect on speed. The equivalent rotational inertia Jm of motor-transmission chain-load has the biggest influence on acceleration;the second is the resistance of motor;the inductance L of motor has almost no effect on acceleration. Speed sensitivity is verified by perturbation method,and the obtained conclusion is the same as trajectory sensitivity method.