White matter, a densely packed collection of myelinated axons, plays an essential part in neural networks. With high spatial resolution and deep penetration, multi-photon microscopy (MPM) is promising for white matter imaging in animal models in vivo. The third harmonic generation (THG) signal can be generated from white matter, but the bottom part of the white matter layer generates weak THG due to its high scattering. Here, we demonstrate an in vivo labeling and imaging technology, capable of visualizing the white matter layer in the mouse brain, combining fluorescence labeling with MitoTracker Red and three-photon fluorescence (3PF) microscopy excited at the 1700 nm window. 3PF signals are several times higher than THG signals, resulting in deeper imaging of the white matter layer with the former. Our results indicate that 3PF microscopy is a promising technology for white matter imaging in the deep brain in vivo.