Treatment of port wine stain (PWS) by photodynamic therapy (PDT) has been under development over last years. To study the acting factors on vascular selectivity of photodynamic and help the doctor confirm therapy plan in clinic, the mathematics modeling of photodynamic therapy treating port wine stain is built. The modeling include light distribution in tissue, production of singlet oxygen, diffusion of photosensitizers and photobleaching. Using the model, a problem of therapeutic effect in clinic is analyzed and a new therapy scheme is recommended. The scheme is proved to be effective in the clinic experiment.