MEMS-based LiDAR with a low cost and small volume is a promising solution for 3D measurement. In this paper, a reconfigurable angular resolution design method is proposed in a separate-axis Lissajous scanning MEMS LiDAR system. This design method reveals the influence factors on the angular resolution, including the characteristics of the MEMS mirrors, the laser duty cycle and pulse width, the processing time of the echo signal, the control precision of the MEMS mirror, and the laser divergence angle. A simulation was carried out to show which conditions are required to obtain different angular resolutions. The experimental results of the 0.2° × 0.62° and 0.2° × 0.15° (horizontal × vertical) angular resolutions demonstrate the feasibility of the design method to realize a reconfigurable angular resolution in a separate-axis Lissajous scanning MEMS LiDAR system by employing MEMS mirrors with different characteristics. This study provides a reasonable potential to obtain a high and flexible angular resolution for MEMS LiDAR.