E-commerce has grown exponentially in the past decade in global market. In China most E-commerce enterprises are small and medium-sized (SMEs). Compared to their large-sized counterparts, SMEs have to face many obstacles when extending their E-commerce businesses. In view of the complexity and periodicity of criteria in SMEs’ development, the paper develop an evaluation method using complex fuzzy sets (CFS) to help them select appropriate development path. Then the paper focuses on a case study in Chongqing, China and compares the results with two other different methods (TOPSIS and COPRAS). The study indicates that the presented work can better handle uncertainty and periodicity in the evaluation process.