Three‐photon fluorescence (3PF) imaging is an emerging technology for imaging deep‐tissue submicroscopic structures by nonlinearly redshifting the excitation wavelength to the second near‐infrared (NIR‐II) window; thus, this approach has great advantages, including deep penetration depth, good spatial resolution, low background, and a high signal‐to‐noise ratio. 3PF imaging has been demonstrated to be a powerful tool for noninvasively visualizing all kinds of deep tissues in recent years. Benefiting from excellent biosecurity and structural controllability, the development of organic 3PF probes is highly important for advancing 3PF imaging in vivo. However, there is no summary of the generalizability of the design and recent progress in organic 3PF probes. Herein, this review introduces the fundamental principle of 3PF imaging and highlights the advantages of 3PF bioimaging. The molecular design of these organic 3PF probes is also summarized based on relative optical indices. Furthermore, different 3PF imaging application scenarios are listed in detail. In the end, the main challenges, significance of probe exploitation, and prospective orientation of organic probes for precise 3PF imaging are proposed and discussed for promoting future applications and clinical translation.