A skin optical diagnosing apparatus and operating method thereof are disclosed. The skin optical diagnosing apparatus includes a positioning module, an optical sensing module, a processing module, and a display module. The skin optical diagnosing apparatus uses the positioning module to select a target region on a sample, and then the optical sensing module performs an optical sensing on the target region to obtain an optical information data related to the target region. The processing module is used for processing the optical information data to generate an optical diagnosed result. The display module is used for displaying the optical diagnosed result.