To improve the pointing accuracy of mobile photoelectric telescopes with inertial navigation systems (INSs), a modified inertial pointing and control system is proposed, where the inertial measurement units are transferred from the motion platform to the pointing instrument. As a result, the INS is decoupled from the platform. This paper firstly utilizes coordinate transformations to establish the measurement equations for a mobile telescope system with two structures respectively. Next, an exhaustive error analysis is performed, which involves identifying the error sources and corresponding distributions. Accordingly, the Monte Carlo method is adopted to synthesize and evaluate the pointing error. The simulation results indicates that the mobile photoelectric telescopes with improved structures achieve better pointing accuracy without highly accurate shaft angle encoders, thus simplifying the design and affording greater reliability. Specifically, In terms of means, the systematic error is reduced by over 97%; with standard deviation, the elevation random error is reduced by about 62%.