The invention relates to an automatic signal delay compensation method and system suitable for a radiation effect test. The system provided by the invention comprises a clock phase adjusting module, a verification vector generation module and a delay compensation judgment module. According to the method provided by the invention, signals in long-line transmission are acquired by adopting a clock capable of adjusting phase, the phase of the sampling clock is adjusted to the degree that the signals have enough leading edge margin and lagging edge margin, the signals in long-line transmission can be accurately acquired, and signals synchronous with a system clock can be obtained by acquiring the signals (acquired by the sampling clock) by the system clock. According to the invention, the signal delay problem caused by long-line transmission in the radiation effect test can be solved, field debugging of the test system in a radiation environment caused by long-line data transmission can be avoided, and the test system has adaptive capability for different test environments.