In order to realize the miniaturization and digitization design of ground penetrating radar (GPR), this paper studies the design of pseudo-random (PRN) coded GPR system. A dual-channel pseudo-random coded ultra-wideband (UWB) GPR controller is presented in this paper. A dual-channel golay complementary pairs coded signal with a center frequency of 60MHz and 800MHz is transmitted and received by using the symbol balanced direct transmission signal source design based on the Virtex-5 and space-level ADC chip ADS5463-SP. The signal source test and the closed-loop test of the controller are carried out. The peak sidelobe ratios of the two-channel pulse compression results are greater than 25dB, and the distance resolution of 1.875m in low frequency and 11.72cm in high frequency is achieved. The controller is connected to the radar system, and the high frequency channel test is carried out in a sand pit. The thickness of the buried marble slab is measured to be about 17cm. The results show the performance of the radar controller designed in this paper is reliable, and it can be widely used in the PRN UWB GPR system.