Integrated systems are facing complex and changing environments with the wide application of atmospheric LiDAR in civil, aerospace, and military fields. Traditional analysis methods employ optical software to evaluate the optical performance of integrated systems, and cannot comprehensively consider the influence of optical and mechanical coupling on the optical performance of the integrated system, resulting in the unsatisfactory accuracy of the analysis results. Optical–mechanical integration technology provides a promising solution to this problem. A small-field-of-view LiDAR system with high repetition frequency, low energy, and single-photon detection technology was taken as an example in this study, and the Zernike polynomial fitting algorithm was programmed to enable transmission between optical and mechanical data. Optical–mechanical integration technology was employed to obtain the optical parameters of the integrated system under a gravity load in the process of designing the optical–mechanical structure of the integrated system. The experimental validation results revealed that the optical–mechanical integration analysis of the divergence angle of the transmission unit resulted in an error of 2.586%. The focal length of the telescope increased by 89 μm, its field of view was 244 μrad, and the error of the detector target surface spot was 4.196%. The continuous day/night detection results showed that the system could accurately detect the temporal and spatial variations in clouds and aerosols. The inverted optical depths were experimentally compared with those obtained using a solar photometer. The average optical depth was 0.314, as detected using LiDAR, and 0.329, as detected by the sun photometer, with an average detection error of 4.559%. Therefore, optical–mechanical integration analysis can effectively improve the stability of the structure of highly integrated and complex optical systems.