With the rapid development of China’s economy and society, China’s railway transportation system has been dramatically improved in terms of its scale and operational efficiency. To uncover the underlying relationship between urbanization and railway network structure, this paper examines the evolution of China’s railway transportation system from 1999 to 2019 by applying complex network theory. The results show that China’s railway network (CRN) has become more connected, more “small-world” and more heterogeneous since the beginning of the twenty-first century. Based on the train flow and train travel distance, the evolutionary course of CRN is found to undergo two apparent stages, with a turning point in 2007. By calculating the regional railway connection index (RRCI), it is revealed that the planned core cities in different regions act as bridges connecting the regions to the rest of the whole network.