This paper addresses the application of multimodal nonlinear optical (MNLO) microscopy to clinical research within the context of label-free non-invasive molecular imaging. Here, a compact MNLO microscope based on a laser scanning microscope, a femtosecond laser, a time-correlated single-photon counting system, and a photonic crystal fiber are introduced for biomedical applications. By integrating two-photon fluorescence, two-photon fluorescence lifetime imaging, second-harmonic generation, and coherent anti-Stokes Raman scattering microscopy, the proposed scheme provides profound insights into the physicochemical properties related to 3D molecular orientation distribution, inter- and intra-molecular interactions, and disease progression in biological systems and organs. The high peak power and the low average intensity of near-infrared laser pulses allow for deep-penetration imaging without compromising sample vitality. Linking nonlinear optical phenomena with time/spectral/polarization-resolved imaging also makes it possible to obtain multidimensional information to address complex biomedical questions.