Balancing network accessibility (node value) and station-area land use (place value) has been an important research topic for transit-oriented development, but little was known about how node and place value should coordinate with ridership. Using Tokyo as a case study, we develop a node-place-ridership model to evaluate coordination between these three facets and compare different transit operators, namely subway in central area, private railway in suburban area, and Japan Railway (JR) in both central and suburban area. An indicator framework is established to measure the node value by accessible opportunities, network centrality, and train service, and measure the place value by density, design, and diversity. Using open-source urban data, we generate a series of node and place indicators for each station and develop a composite node value index and place value index with information entropy weighting. The results show that node value and place value have positive impacts on ridership and node value’s impact is five times higher than place value. Stations balanced between node and place value can be uncoordinated with ridership, while stations unbalanced between node and place value can coordinate with ridership. JR has better node-place balance and ridership coordination than subway and private railway. Several implications are drawn for ridership coordination with node and place value, including planning for a more mixed urban structure and using through trains to connect central and suburban transit networks. The results of this study would inform transport planners of better organizing transit network, land use, and ridership in urban space.