Epithelial cancer comprises more than 85% of human cancers. The detection and treatment at the early stage has been demonstrated to apparently improve patient survival. In this review, we summarize our recent research works on the diagnostic application of epithelial tissue based on multiphoton microscopy (MPM), including identification of the layered structures of esophagus, oral cavity, skin and bronchus tissues, establishment of the diagnostic features for distinguishing gastric normal tissue from cancerous tissue, linking collagen alteration and ectocervical epithelial tumor progression for evaluating epithelial tumor progression, and differentiating normal, inflammatory, and dysplastic ectocervical epithelial tissues. These results provide the groundwork for developing MPM into clinical multiphoton endoscopy.