Due to the precursor gas flow in the focused ion beam induced deposition process, a shadow effect appears behind the shading structures. This article carries out experiments with phenanthrene as the precursor gas and establishes a numerical model to define the shadow area and estimate the intensity of the shadow effect, considering the morphology of shading structure, the beam shift, and the nozzle parameters. Within the shadow area, the precursor molecule adsorption contribution is estimated by calculating the fraction of precursor gas flow in a specific direction. Finally, the number of precursor molecules within the beam impact area influenced by the shadow effect is obtained, emphasizing the important role of gas surface diffusion. The adsorption contribution within the shadow area differs a lot while deposited structures are similar in height. The error between the simulation and the experimental results is about 5%, verifying the accuracy of the proposed model.