The light screen projectile velocity measurement system is widely used in the field of flying object velocity measurement and weapon testing, but its velocity measurement accuracy is largely limited by the timing accuracy of the system. This paper proposes and builds an light screen projectile velocity measurement system based on field programmable gate array and multi-phase clock time-to-digital converter. Its timing resolution reaches 312.5 ps, timing accuracy reaches 125.6 ps, and the maximum timing range reaches 1.342 s. At the same time, in view of the limitations of the existing simulation test scheme of light screen velocity measurement system with less sampling and slow response, this paper designs a simulation test scheme of high speed response based on picosecond pulse laser, and obtains that the time measurement accuracy of this velocity measurement system is better than 85 ns. When the projectile velocity is 1000 m/s, the theoretical measurement accuracy of the velocity measurement system can reach 0.085‰. In addition, the working state of the system is verified by the projectile firing test. The results show that the system has simple structure, low cost, high timing accuracy, and high scalability, which provides a feasible scheme for improving the measurement accuracy of the light screen velocity measurement system.