Differential image motion lidar is used to measure profiles of atmospheric turbulence. A formula is deduced to quantify the error of differential image motion variance, which provides the basis of qualitative analysis and improvement of system performance. With reasonable arrangement of distance resolution and time resolution, the best measurement results can be obtained. According to analysis, two mainly error sources are the errors from centroid position of image and statistical uncertainty of finite sample. The simulation results show that statistical error is the dominant factor at lower altitude, while centroid calculation error plays an increasingly important role with the increasing of distance.