Lidar system is a powerful equipment of remote sensing with high spatial and temporal resolution and accuracy, which is widely used in atmospheric detection in regional or global scales. Overlap factor is an important factor that affects atmosphere detection with lidar system at near range. The accurate calculation is helpful to obtain more accurate detecting results. The overlap factor calculation method based on the laser intensity distribution is simple and practical. The algorithm not only applies to any specific laser intensity distribution, but also to results simulation with different initial parameters setting. Overlap factors are calculated with this algorithm, and calculation results are compared with experimentally measured overlap factor derived from the lidar signal. Moreover, we analyzed the influences of the system parameters on overlap factor and the sensitivity of the overlap factor. The results provide a certain reference to system debugging, optimization configuration and error control of lidar.