Research on the changes of structure characteristics and optical properties of the port wine stain (PWS) skin after photodynamic therapy (PDT) can evaluate the treatment effect objectively and provide reference for the clinician to adjust the protocol. Based on optical coherence tomography (OCT), the structure characteristics and scattering properties of the PWS skin are measured. Through analyzing the OCT signal characteristics shown in epidermis, dermis and blood, the thickness of epidermis, the diameter and depth of ectatic vessels in the PWS skin before and after PDT are calculated. An optical properties extraction algorithm is developed based on extended Huygens-Fresnel light propagation theorem, to extract the scattering coefficience of the PWS skin before and after PDT. The parameters of 28 PWS patients obtained before and after PDT are compared. The results show that the changes of epidermis thickness and scattering coefficients are not obvious (p>0.05). However, the mean ectatic vessels diameter is decreased and the locations of ectatic vessels in OCT images are deeper than those before PDT (p<0.05). This study indicates that OCT can be used as a noninvasive and in vivo measurement method to evaluate the structure and optical properties of PWS skin. The conclusions imply that this measurement method can be used to evaluate the treatment outcome and adjust PDT protocol individually.