Understanding the difference of foreign trade structure between cities is of great value to understand their difference in foreign competitiveness and their roles in international division. However, few theoretical and empirical literatures investigate this issue. This paper computes four trade structure indices (ownership, trading type, geography and product) of prefecture-level cities in China using data from “China Customs Import and Export Statistics Database” between 2000 and 2008 and shows that there are significant differences between them. Combined with “China City Statistical Database”, this paper shows that technology, factor endowment, internal geography, agglomeration economies and human capital are import factors forming these differences.