A method for analyzing mucosa structure with optical coherence tomography (OCT) is provided, and includes: (a) scanning a mucosa sample with optical coherence tomography; (b) choosing a lateral range from a two- or three-dimensional OCT image and analyzing all the A-scan intensity profiles in the lateral range; (c) calculating three indicators in each A-scan intensity profile, including the standard deviation for a certain depth range below the sample surface, the exponential decay constant of the spatial-frequency spectrum and the epithelium thickness under the condition that the basement membrane is identifiable; and (d) using the three indicators of each A-scan intensity profile within the lateral range to analyze the mucosa structure.