The popularity of electric bicycles in China makes them a common transportation mode for people to commute and move around. However, with the increase in traffic volumes for both vehicles and electric bicycles, urban traffic safety and congestion problems are rising due to traffic conflicts between these two modes. To regulate travel behavior, it is essential to analyze the mode choice and route choice behaviors of travelers. This study proposes a combined modal split and multiclass traffic user equilibrium model formulated as a complementarity problem (CP) to simultaneously characterize the mode choice behavior and route choice behavior of both vehicle and electric bicycle users. This model captures the impacts of route travel time and out-of-pocket cost on travelers’ route choice behaviors. Further, modified Bureau of Public Roads (BPR) functions are developed to model the travel times of links with and without physical separation between vehicle lanes and bicycle lanes. This study also analyzes the conditions for uniqueness of the equilibrium solution. A Newton method is developed to solve the proposed model. Numerical examples with different scales are used to validate the proposed model. The results show that electric bicycles are more favored by travelers during times of high network congestion. In addition, total system travel time can be reduced significantly through physical separation of vehicle lanes from electric bicycle lanes to minimize their mutual interference.