Aerosol backscatter signal of laser diode ceilometer, acquired by using APD detectors, has relative low SNR, which can not be directly used for inversion of atmospheric parameters such as cloud height, vertical visibility. A timing control and signal processing scheme of laser diode ceilometer is presented, aiming at the characteristics of backscatter signal. AD converter performs high speed data acquisition, and then DSP finishes cumulative average. Meanwhile, the complex timing control of the whole system’s transmitting receiving, maintenance, data saving, and uploading is performed. The comparison experiments show that the scheme works well, and can significantly improve the backscatter signal’s SNR to help the inversion of atmospheric parameters.