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Two-photon microscopy (TPM) has been one of the most widely used fluorescent microscopy methods in biological tissue. The femtosecond laser in the near-infrared (NIR) range showed better penetration in tissue due to less scattering and absorption. The method to estimate the optimal wavelength generally according to the scattering and absorption is somehow too rough considering the complex biological property and other factors that influence TPM. In this report, we set up a model to calculate the optimal wavelength in the NIR range for different imaging depths by involving more parameters of TPM. The calculated result suggests the image of brain slice stained with fluorescein isothiocyanate (FITC) can be acquired with the best TPM imaging quality at 780 nm excitation rather than longer wavelengths, which is consistent with our experimental results of TPM at depth of 50-300 μm in mouse brain tissue. Our results may, therefore, bring a better understanding on TPM in tissue and help to develop a more accurate model for the simulation of TPM.