In this study, an integrated synchronous data acquisition subsystem for high-speed dual-channel ultra-wideband ground penetrating radar (GPR) system is designed and tested. Factors that could cause data missing and asynchronisation are analyzed. According to timing sequence, a field-programmable gate array-based onboard digital control module is integrated to synchronise the data acquisition and data storage subsystems. By applying simultaneous multi-buffer acquisition and readout mode and multi-threading configuration, as well as the critical section control and queue storage structure, the GPR data throughput is considerably improved. For the practicality of this system, a smart End-of-Job control design is performed between different threads to control data acquisition. By using different performance indexes, receiver operation characteristic curve, maximum scan rate, and the rebar detection experiment demonstrate the superiority of author's method.