The Tokyo Metropolitan Area Convection Study (TOMACS) for extreme-weather-resilient cities is a research and development project (RDP) of the World Weather Research Programme (WWRP). TOMACS provided a multiplatform and high spatiotemporal resolution dataset for the present research on three episodes of deep convection in the Tokyo Metropolitan Area (TMA) under its heat island effect and sea breeze circulations. Heavy rainfall episodes of August 26, 2011, and July 23 and August 12, 2013, were simulated with (and without) the tropical town energy budget (T-TEB) model coupled with the advanced regional prediction system (ARPS). The T-TEB/ARPS system used initial and boundary conditions from the Japan Meteorological Agency (JMA) mesoscale analysis data for 24-hour integration runs at 5-km resolution over Japan and at 1-km resolution over TOMACS area. The 1-km resolution hourly rainfall field simulations were verified against the respective automated meteorological data acquisition system (AMeDAS) rain gauge network measurements. Statistics of the Contingency tables were obtained to estimate the critical success index (CSI), probability of detection (POD), and false alarm rate (FAR) as well as the root mean square error (RMSE). The T-TEB/ARPS simulations improved the south and east sea breeze circulations of TMA and its urban heat island effect. The time evolution of CSI scores improved within the advective time scale, whereas dissipation (phase) errors on precipitation RMSE increased with the integration time and were larger than the dispersion (amplitude) errors. The initial and boundary conditions of JMA greatly improved the simulations as compared to the previous ones performed with the outputs of NCEP’s global forecast system as indicated by the TOMACS datasets. Thus, the results represent the temporal and spatial evolutions of the atmospheric conditions leading to the development of a deep convection within TOMACS region. Furthermore, TMA is a good testbed to evaluate the urban surface schemes, such as T-TEB in this study.