Understanding the mechanism of continuous subscribing behavior is vital to the operation and even survival of customized bus (CB) systems. Capturing the differences in subscribing behavior of active and inactive users and developing targeted and differentiated marketing strategies accordingly will help to improve the user retention rate. The results of this study revealed differences in the subscribing behavior between active and inactive users and the influence of a wide range of factors on the subscription behavior between the two groups, such as area-related and individual characteristics. Travel distance presents an inverted “U” shape effect on the propensity to use CB with the vertex at around 16 km for active users and 28 km for inactive users, which is a further finding of the monotonic positive effect indicated by the existing studies. For every RMB 10 cheaper CB trip, the likelihood that an active user holds a higher “propensity” to use CB services will increase by 8%. The cost advantage will attract novelty-seeking travelers to try CB services occasionally, but cannot convert them into high-frequency users. The passengers who started to subscribe to the CB service in winter are more likely to travel by CB frequently no matter in active and inactive user groups. The findings of this empirical study lay a theoretical foundation for ridership retention and marketing orientation of the customized and demand-responsive transit services.