The passenger flow effects are the core issue of rail transit development. In this study, we analyzed the characteristics of passenger flow distribution in the Shenzhen rail transit network and discussed the rail transit passenger flow pattern, based on Shenzhen IC card swiping data. We then proposed, based on the flow intensity and time sustainability, a comprehensive index to quantitatively evaluate the passenger flow vitality of the Shenzhen metro stations and classify them accordingly. The results show that the passenger flow distribution of the Shenzhen rail transit network is extremely unbalanced, with the top 10 stations capturing a large proportion (19.64%) of the passenger flow. There are significant differences in the passenger flow patterns of different types of stations, and differences between working days and non-working days are also apparent. Over 60% of the Shenzhen rail transit stations show relatively low vitality, however the passenger flow on non-working days is significantly better than on working days.