Since the initiation of the China-Europe Railway Express (CR Express) in 2011, with important milestones such as the Belt and Road Initiative (BRI) proposed in 2013 and the release of the China-Europe Railway Express Development Plan in 2016, CR Express’s development can be roughly divided into three phases: the exploration period, the vigorous development period, and the standardization and enhancement period. During the exploration phase, China State Railway Group Co., Ltd. primarily faced challenges such as optimizing the organization of train transport processes and improving customs clearance and inspection and quarantine efficiency. In the prosperity phase, China Railway’s operation of the CR Express was primarily constrained by the insufficient return cargo sources, leading to a decline in key technical and economic indicators for the trains. In the standardization and enhancement phase, balancing the interests of localities and China Railway and maximizing the brand value of the CR Express became new challenges for China Railway. Therefore, a systematic review of the institutional changes and evolutionary mechanisms of China Railway’s operation of the CR Express holds significant importance for further standardizing and enhancing the quality and level of the China-Europe freight train services.