Based on analysis of the relation between mean penetration depth and source-detector separation in a three-layer model with the method of Monte-Carlo simulation, an optimal source-detector separation is derived from the mean penetration depth referring to monitoring the change of chromophores concentration of the sandwiched layer. In order to verify the separation, we perform Monte-Carlo simulations with varied absorption coefficient of the sandwiched layer. All these diffuse reflectances are used to construct a calibration model with the method of partial least square (PLS). High correlation coefficients and low root mean square error of prediction (RMSEP) at the optimal separation have confirmed correctness of the selection. This technique is expected to show light on noninvasive diagnosis of near-infrared spectroscopy.