To quantitatively analyze the relationship between plant canopy structure and light distribution and photosynthesis, simulate real time photosynthetic rate of plant canopy in actual environments, and prove a plant canopy scale photosynthetic productivity calculation method for crop yield estimation, a 3D virtual plant canopy photosynthesis simulation model was constructed based on L-system. The model was divided into three contents. The first submodel was the 3D virtual canopy based on L-iterative grammar system and 3D graphic rendering technology. The second sub-model was that the photosynthetically active radiation (PAR) transformation in the virtual canopy was simulated by using forward ray tracing and sky visibility algorithm. The third sub-model was that the real-time PAR intensity at the top of a virtual canopy based on parameters such as the sun’s geometric parameters, atmospheric influence parameters and geographic location. After the photosynthetic environmental factors were directly or through interpolated way to input to the sub-models, by using the single leaf photosynthesis model and related respiration models, the net photosynthesis rate within the canopy and the accumulation of plant biomass accumulation during the model simulation cycle can be calculated. The simulation results of Chinese fir showed that the simulation of the PAR distribution based on the virtual canopy and the canopy photosynthesis rate calculation was an effective method for estimating photosynthetic productivity of plants.