Recently, there are two mainly methods for SMEs operating cross-border e-commerce in China. One is online store of firms via the cross-border third party platform. The other is the online store of firms built by themselves for export markets expansion. Based on the analysis of cross-border e-commerce process, we explore four factors which may affect the mode selection of cross-border e-commerce of SMEs, namely E-marketing, electronic payment, electronic customs and international logistics. For the methodology, we use Probit model of Logit modeling and then have the finding that the three factors E-marketing, electronic customs and international logistics are the impact of SMEs cross-border e-commerce mode selection, and further find that most of SMEs who are weak at cross-border e-commerce operation stay on third party cross-border e-commerce service platform. Based on the finding, we also have some conclusion. In order to assist SMEs development, the government should establish and improve the trade informational platform. Meanwhile, they should encourage the cross-border e-commerce third-party platform to become bigger and stronger and improve electronic customs clearance continuously to raise large scale cross-border logistic firms and third parties with good service, strong competition and high technologies. For the SMEs, they should adopt the third party cross-border e-commerce platform actively. Some firms should have their own cross-border websites for opening cross-border e-commerce channel actively.