The China-Europe Railway Express and the Southbound Railway Express are significant initiatives for optimizing China’s regional open-layout strategy. Analyzing their logistics spatial linkages is conducive to integrating and coordinating the logistics resources of node cities. Based on the actual data of 51 node cities of the China-Europe Railway Express and an additional 24 node cities of the Southbound Railway Express, this paper constructs a cross-border railway transport network. The entropy weight TOPSIS comprehensive evaluation method is employed to measure the logistics development level of cities, and a modified gravity model is used to study the logistics spatial linkages between cities. The results show that there are significant differences in the logistics development levels of node cities in the cross-border railway transport network. The logistics linkages among these cities are mainly characterized as weak, moderately weak, and moderate, with fewer strong and very strong linkages. Overall, the network exhibits distinct regional agglomeration features, primarily concentrated in four major areas: the Pearl River Delta, the Yangtze River Delta, the Western Triangle Economic Circle, and the Bohai Rim. To further optimize the structure of the cross-border transport logistics network, this paper ultimately selects Shenzhen, Suzhou, Chongqing, Chengdu, Xi’ an, Jinan, and Wuhan as logistics hub cities, with Yiwu and Nanning as alternative hub cities.