After more than 20 years of development, miniature two-photon microscope and endomicroscope technology have shown important application value in the field of in situ three-dimensional pathological detection and brain imaging of free walking animals (such as mice). In this paper, centering on two representative technological approaches—fiberscanning two-photon endomicroscope and head-mountable two-photon microscope, the core principles and methods of the miniaturized two-photon (endo)microscope imaging system are systematically described, focusing on the following key technical challenges and solutions: 1) efficient delivery and focusing of excitation light; 2) optimized collection of backscattered signals; 3) miniaturized distal-end scanning mechanism. Finally, the representative applications of this technology in neuroscience and clinical medicine are summarized, and its future development trends are briefly discussed.