Pure Rotational Raman Lidar is a recently developed method for atmospheric temperature detection. Since the Raman-scattering-signals are very weak, the photon-counting method is employed, which could be achieved by using a multiscaler. Time delays, which exist among the trigger channel and the two count channels of the multiscaler, will affect the corresponding relationship between the detected signals and the actual altitudes where the signals are returned, so it is necessary to make some compensation. However, it is difficult to measure the time delays with traditional instruments such as oscillograph, for there is no access to the final internal trigger signal or count signals. In this paper, a measuring system is established, with a Digital Delay/Pulse Generator as the chief component, which is not usually used as a measuring instrument. The measurement precision could reach about 50ps. Meanwhile, the compensating method is also provided to improve the positioning accuracy of the lidar system.