Abstract: A three-layer emotion model structure based on brain science was proposed firstly.Then a bottom-level emotion model of the intelligent system was presented in detail.It was constructed by using fuzzy mathematics and matrix description of finite state machines.A fuzzy relation between stimulus and emotion was produced to determine the active emotion in consideration of mood and desire at that time.The output behavior was calculated by a matrix style of finite state machines while the active emotion was given.The model constructed in this way could reduce memory spaces used only for storing the corresponding relations among stimulus,emotion and behavior.The simulation result and conclusion are presented in the end.