The invention relates to the technical field of spacecraft autonomous navigation, in particular to a ground test signal control system for X-ray pulsar navigation. The control system comprises a database module, a time delay module, a pulsar numbering module, a period control module, a stable time module, a communication module, a static random access memory (SRAM) data temporary storage module, a FLASH data storage module, a digital-to-analogue conversion module, an address coding module, a low-pass filtering module, a power amplification module, a phase increment storage module, an addition module, a phase accumulation module and a peripheral equipment X-ray source. The control system is suitable for an X-ray pulsar navigation ground test verification system, and is used for ground semi-physical closed loop verification of relative key techniques of the X-ray pulsar navigation, such as calibration of a space X-ray probe, extraction of a pulse profile, measurement of pulse phases, confirmation of pulse arrival time, large-scale space-time basic standards and verification for navigation algorithm.