A high-resolution flight time measurement system based on a single field programmable gate array (FPGA) in laser altimeter is designed. The time resolution of 300 ps is obtained, because the differential delay lines are used to perform interpolation and to realize the fine time measurement, and high frequency counter is designed to perform the coarse time measurement. The time splitting circuit, pulse width counter and data transmitter module are integrated in the same chip. At an ambient temperature of 20 ℃, we achieve a standard deviation of 94.68 ps which equals to 1.42 cm in distance. Furthermore, detection on the ground verifies the feasibility of measuring distance with ±50 cm resolution over 500 km ranges under general conditions.