Aiming at the urgent demand of high-precision optical alignment systems for a domestic infrared focal plane flip chip bonder, an optical alignment system was designed and verified, and the parallel adjustment, optical alignment and coordinate system error compensation algorithms applied to the system were researched. Firstly, this paper analysed the optical alignment process of a flip chip bonder, then introduced the parallelism adjustment and optical alignment algorithm, and proposed a more reasonable error compensation algorithm according to the test process of the optical alignment system. Finally, based on the above calculation algorithm, the optical alignment system was designed including three parts: a collimation system, a microscopic imaging system and a laser ranging system. The functions of parallel coarse adjustment, feature point recognition and parallel fine adjustment were realized. The experimental results show that the collimation system has a good collimation effect, the microscopic imaging system has high resolution and good imaging quality, and the ranging accuracy of the laser ranging system is 0.084 μm. The designed high-precision optical alignment system solves the urgent need of a domestic infrared focal plane flip chip bonder for high-precision optical alignment systems. It has been applied in a certain types of flip chip bonders, and has very important social significance for improving the independent research and development and production capacity of domestic high-end large-scale integrated circuits.