One of the challenges in transcranial low-level laser therapy (LLLT) is to optimally choose illumination parameters, such as wavelength. However, there is sparse study on the wavelengths comparison especially on human transcranial LLLT. Here, we employed Monte Carlo modeling and visible human phantom to compute the penetrated photon fluence distribution within cerebral cortex. By comparing the fluence distribution, penetration depth and the intensity of laser-tissue-interaction within brain among all candidate wavelengths, we found that 660, 810 nm performed much better than 980, 1064 nm with much stronger, deeper and wider photon penetration into cerebral tissue; 660 nm was shown to be the best and slightly better than 810 nm. Our computational finding was in a surprising accordance with previous LLLT-neurobehavioral studies on mice. This study not only offered quantitative comparison among wavelengths in the effect of LLLT light penetration effectiveness but also anticipated a delightful possibility of online, precise and visible optimization of LLLT illumination parameters.