According to the demands of a photoelectric theodolite for angle measurement accuracy, a CCD exposure center measurement system by taking the IRIG-B code terminal as time reference was designed based on a Digital Signal Processor(DSP) and a Field Programmable Gate Array(FPGA). The measuring principle and hardware components of the CCD exposure center were given. Then two sets of IRIG-B terminals with a total source code were used to control a light emitting diode and a CCD detector. By adjusting the B code terminal output signal time delay to control the light-emitting diode, two key moments along with the front and back edges for 1 Hz pulses and the exposure pulses were obtained, respectively. Aiming at the low accuracy of artificial image interpretation, an image edge extraction algorithm based on the image centre and an improved Krisch algorithm were proposed, and the CCD exposure center with a precision better than 17 μs was automatically calculated. Finally, several sets of CCD exposure centers for photoelectric theodolites were measured in the field, and the measurement results were applied to the outfield calibration flight data processing. Obtained results show that the angle measuring error of photoelectric theodolite is reduced by 55% on average in the Czech Airlines time, and the system is stable, reliable and has a wider application prospect.