This study models the equilibrium mode choice of emerging customized bus (CB) services in a multi-modal urban transportation network. Two unique characteristics of CB services are considered: (1) the reservation of a seat for every CB passenger, and (2) the loyalty scheme for long-term CB subscribers. The first characteristic eliminates in-vehicle crowding but imposes tight constraints on CB demand, while the second characteristic encourages passenger loyalty to CB services. An advanced equilibrium mode choice model based on the dogit model, a well-established travel choice model that is widely used to consider captive mode choices, is proposed to account for the choice behavior of passengers loyal to CB services. In contrast, a nested weibit model is used to account for the choice behavior of passengers not loyal to CB services by simultaneously considering the effects of mode similarity and mode heterogeneity on mode choice behavior. The proposed model is formulated as an equivalent mathematical programming problem, which guarantees the existence and uniqueness of solutions. Numerical experiments are conducted to illustrate the properties and applicability of the proposed model in a real-world setting. The results demonstrate the importance of considering passenger loyalty and managing mode similarity and heterogeneity when modeling emerging CB services. The results also show the applicability of the proposed model for evaluating the performance of a network with CB services and the design and pricing of CB operation and subscription schemes.