In the past two decades, two-photon microscopy (TPM) transforms biomedicalresearch, allowing nondestructive high-resolution fluorescent molecular imaging and label-free imaging in vivo and in real time.Here we review the recent advances of TPM technologyincluding novel laser sources, new image acquisition paradiams, and microendoscopicimaging systems. Then, we survey the capabilities of TPM imagingof biological relevant molecules such as nicotinamideadenine dinucleotide (NADH), flavin adenine dinucleotide (FAD),and reactive oxygen species (ROS). Biomedical applications of TPM in neuroscience and cancer detection are demonstrated.