Understanding the determinants of the route choice behaviour on a multi-modal transit network of metro and shared bike is important to improve personalized multimodal travel services. This paper attempts to analyse the route choice behaviour of metro-bikeshare users considering passengers’ socio-economic attributes and perceived congestion which is approximated by load status. An abstract integrated metro-bikeshare network (IMBN) is built with virtual nodes by aggregating shared bike stations within the walkable distance and abstract routes by aggregating optional paths for each OD pair. Using the metro- and shared bike smart- card data from Nanjing, China, the route sets of metro-bikeshare users were extracted from the IMBN. A multinomial Logit model (MNL) was then applied to investigate the determinants of route choice behaviour for two types of users, namely “return-enter” and “exit-lease”, respectively. The results show that the models with the load status attributes have a better performance than the models without these attributes. We found the sensitivity of “exit-lease” users to the train crowding is significantly greater than that of the “return-enter” users. “Return-enter” users have a higher perception of out-of-vehicle travel time (OVTT) than that of in-vehicle travel time (IVT), while the “exit-lease” users have the opposite perception. Besides, the change rate of shared bike inventory, departure time and whether he or she is a regular user also have a significant impact on route choice behaviour. The findings can help policymakers and system operators to improve the services and the efficiency of the multimodal transportation system.