The invention provides a nuclear power station digital instrument control system time calibration method. According to the method, time calibration for a server and a control state of a nuclear power station digital instrument control system carried out by an external clock source, second-level time calibration for the sever is carried out by the external clock source, and millisecond-level time calibration for the control station is carried out; the minute-level and above data of a second-level clock, the second-level and millisecond-level data of a millisecond-level clock are acquired by a control station clock to synthesize the system time of the control station. According to the method, the second-level time sent by the server can be only utilized to the minute-level and above time in the control station, a source of a clock error between any two control stations is generated from millisecond-level time calibration in the control station, and a generation error is 1 millisecond.