Choosing a suitable cross-border logistics mode is the foundation for cross-border e-commerce enterprises to achieve sustainable development. Based on an analysis of the literature, the cross-border logistics modes are summarized as postal parcel, international express, overseas warehouse, and special line logistics modes. Using the multi-value set qualitative comparative analysis (mvQCA) method to explore the factors and formation paths of logistics mode selection of cross-border e-commerce enterprises, the results include the following: (1) The choice of logistics mode is the result of multiple condition variables, and the formation paths of different logistics mode selection vary. (2) The postal parcel mode is most selected by small and medium-sized B2C cross-border e-commerce enterprises; the overseas warehouse and special line modes are most selected by large and medium-sized ones with high logistics service capacity. (3) The international express mode is selected by B2C cross-border e-commerce enterprises of all sizes, and there is no typical formation path. The results indicate that cross-border e-commerce enterprises should have clear positioning and select the most suitable logistics mode, as only in this way can cross-border e-commerce and logistics enterprises jointly achieve sustainable development.