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In this paper, the photon propagation process in human brain tissue and skin tissue with various source and detector separation distances were simulated based on the Monte Carlo method. The human brain model and the skin model that were used in our experiments have live layers and seven layers, respectively. The backscattered intensity from every layer of the human tissue model was obtained by marking the deepest layer that every photon can reach. The simulation results of brain model indicated that the source-detector separation distance should be selected at three centimeters for studies on the actions of the brain nerve cells; in order to be more sensitive to the volumetric changes of capillaries in the skin, the separation distance of source and detector should be approximately eight millimeters. Future work was discussed at the end of the paper.