Fluorescence emission mechanism of biological tissue is very complex, and related researches have very important significance. Spectroscopy of many biological tissues has been used in clinic; this paper attends to study the mechanism and its implementation pulse electromagnetic fields. We than study the pulse electromagnetic field effect on blood brain barrier of rat by fluorescence spectral properties, which caused by the fluorescent material only could through loose membrane, the results show that pulse electromagnetic field could effect the fluorescence properties of brain in rats, mechanisms of these phenomena also analyzed.