Differences exist among the trigger channel and two count channels of multiscaler, which is an essential component of the rotational Raman lidar system for atmospheric temperature measurement, both in the threshold and time-delay aspects, and they will impact the temperature measurement results. A measuring system is established for the threshold differences, based on the working principle of the multiscaler and the voltage fluctuation of square waves. In the measuring system, square waves with different voltage values are input to the two count channels successively. Through changing the set threshold value, the count value will be at the peak under a particular set threshold value. By this way, pairs of respective set threshold values of the two count channels corresponding to the same input square wave can be obtained, and furthermore the threshold curves can be fitted. One more measuring system is established for the time-delay differences, and the method for compensating the differences is also proposed. Analysis shows that with the threshold value set according to the fitted curves, the appropriate thresholds can be set more quickly, and the positioning accuracy of atmospheric temperature profile can be improved by about 10 m with the time-delay differences compensated.