Abstract: Based on the frequency data of high-speed rail services from the 12306 Chinese Timetable website and the complex network theory, this paper analyzes the spatial distribution characteristics of the high-speed rail network in the Yangtze River Delta in detail by investigating some indexes, such as dominance index, the service frequency of the stations as starting station, the time distribution of train services, and so on. The result firstly shows that the degree distribution of high-speed rail network has a two-tier hierarchical structure, and the stations can be divided into two types, “degree greater than 60” and “degree less than 60”. Secondly, the high-speed rail exerts a promoting effect on the commuting between Shanghai, Nanjing, Hangzhou and their surrounding cities. Thirdly, a great difference in the grade of stations is found, three high-speed railway stations, Shanghai Hongqiao, Nanjing South and Hangzhou East are the dominant among those stations. Then this paper divides the study area into four closely related communities, and the organizational structure of those communities can be described as multi-level network, sparse network, group network and group with typical core. Finally, the formation mechanism of the above conclusions is discussed.