Intrinsic photopeak efficiency of pixelated CdZnTe detectors is an important property for quantitative measurements and analysis, especially for detection and characterization of special nuclear material (SNM). The intrinsic photopeak efficiency of a single 20 mm × 20 mm × 15 mm CdZnTe detector from 59 keV to 2614 keV are measured in experiment. However, compared to the simulated ideal intrinsic photopeak efficiency, the measured efficiency showed deficit. A detailed simulation model including gamma-ray interaction physics, readout electronic as well as signal reconstruction process is built to explain this observed efficiency deficit. The simulated efficiencies of the new model match with experimental results well after taking these factors into account. Efficiency loss due to the guard ring and anode side inaccurate reconstruction are the most important factors. Other miscellaneous efficiency loss mechanisms are discussed too.