According to the existing problems involving environmental performance evaluation of Small and Medium-Sized Enterprises(SMEs), an evaluation indicator system of environmental performance in SMEs is established in view of evaluation indicator system design principle, which is composed of environmental management performance, operational performance, environmental condition, and environmental profit. A dynamical model on environmental performance evaluation of SMEs based on the secondary relative profit is put forward, which is combined with the basic idea of DEA and GA-BP assessment method. In order to provide the reasonable basis for SMEs taking corresponding measures to improve their environmental performance level, the empirical analysis about 10 SMEs’ environmental performance is carried through and a conclusion is drawn.