High repetition rate lidar is typically equipped with a low-energy, high repetition rate laser, and small aperture telescopes. Therefore, it is small, compact, low-cost, and can be networked for observation. However, its data acquisition and control functions are generally not specially designed, and the data acquisition, storage, and control programs need to be implemented on an IPC (Industrial Personal Computer), which increases the complexity and instability of the lidar system. Therefore, this paper designs an integrated off-line echo signal acquisition system (IOESAS) for lidar developed based on SoC FPGA (System-On-Chip Field Programmable Gate Array). Using a hardware–software co-design approach, the system is implemented in a heterogeneous multi-core chip ZYNQ-7020 (integrated FPGA and ARM). The FPGA implements dual-channel echo data acquisition (gated counting and hardware accumulation). At the same time, the ARM performs laser control and monitoring, laser pointing control, pulse energy monitoring, data storage, and wireless transmission. Offline data acquisition and control software was developed based on LabVIEW, which can remotely control the status of the lidar and download the echo data stored in IOESAS. To verify the performance of the data acquisition system, IOESAS was compared with the photon counting card P7882 and MCS-PCI, respectively. The test results show that they are in good agreement; the linear correlation coefficients were 0.99967 and 0.99884, respectively. IOESAS was installed on lidar outdoors for continuous detection, and the system was able to work independently and stably in different weather conditions, and control functions were tested normally. The gating delay and gating width time jitter error are ±5 ns and ±2 ns, respectively. The IOESAS is now used in several small lidars for networked observations.