Due to atmospheric instability, various noise and sky background radiation of photoelectric detector, the semiconductor laser ceilometer APD detector receives the backscatter signal with low signal noise ratio (SNR) which cannot be directly used for parameter inversion of cloud. So for this characteristic of the backward scattering signal, a data collection and processing scheme of the semiconductor laser ceilometer based on FPGA was proposed. This scheme can achieve the DC blocking of backward scattering signal, high-speed data acquisition, cumulative average, and at the same time it can complete complex sequential control, such as the whole system transmitting and receiving, data storage and upload. Compared with the experimental verification, the scheme can obviously increase the SNR of the backward scattering signal, and achieve the parameters inversion of atmospheric cloud.