For ground-based lidars in atmospheric observation, their data acquisition unit and control unit usually work independently. They usually require the cooperation of large-volume, high-power-consumption Industrial Personal Computer (IPC). However, the space-borne lidar has high requirements on the stability and integration of the acquisition control system. In this paper, a new data acquisition and lidar control system (DALCS) was developed based on System-on-Chip Field-Programmable Gate Array (SoC FPGA) technology. It can be used in lidar systems with high repetition rate and photon-counting mode and has functions such as data storage, laser control, automatic collimation, wireless communication, and fault self-test. DALCS has two working modes: in online mode, the echo data collected by DALCS are transmitted to the computer for display in real-time and then stored with the current time as the file name; in offline mode, the data are stored in local non-volatile memory, which can be read remotely and can work autonomously when there is no IPC. The test results showed that in the frequency range of 0–70 M, the counting linearity of DALCS reached 0.9999, and the maximum relative error between the DALCS card and the standard signal source was 0.211%. The comparison results showed that the correlation coefficient between DALCS and MCS-PCI was as high as 0.99768. The DALCS was placed in a self-developed lidar sensor system for continuous observation, and the system worked stably under different weather conditions. The range-squared-corrected signal profiles obtained from the observations reflect the spatial and temporal distribution characteristics of aerosols and clouds well. This provides scheme verification and experimental support for the development of space-borne lidar data acquisition and control system.