Single photon counting detection technology has become an important development direction in the field of 3D imaging because of its high sensitivity. Complex targets have become important research objects because of their diverse structures and rich features, but their response mechanism of photon imaging is too complex to be analyzed by simple models. In this paper, a single photon 3D imaging data simulation method based on 3D model is proposed for the feature analysis of complex targets. Based on the typical Avalanche Photodiodes (APD) single photon detector array, combined with the single photon 3D imaging detection model, a single photon detection data simulation method based on 3D structure model of complex target is proposed. Firstly, the object body coordinate system was established and the 3D structure was transformed to the imaging coordinate system at fixed point according to the affine transformation model. Then, according to the imaging relationship, the different resolution units in the field of view were divided into background units, foreground units, target units and noise units. The original photon data was generated for different units according to the photon number Poisson distribution model. Through computer simulation, the method is applied to simulate single photon 3D imaging detection data of typical civil aviation targets, laying a theoretical and data foundation for 3D measurement and structural characteristic analysis of targets.