The Tokyo metropolitan area, underlain by Neogene and Quaternary sediments more than 5 km thick, is currently deformed by blind thrusts that could generate hazardous earthquakes. However, their little geomorphic expression and dense urbanization make understanding of folds produced above them and recent deformation highly elusive. Here we show subsurface geometries of several active blind thrusts beneath this highly urbanized area, based on tectonic landforms, high-resolution seismic reflection data, and Quaternary stratigraphy. Deep seismic reflection profiles corroborate the notion that steeply dipping blind thrusts are reactivated normal faults originally formed by middle Miocene extensional tectonics. Despite very slow (less than 0.1 mm/yr) late Quaternary slip rates, our work suggests the presence of previously unrecognized faults that pose seismic hazards to Tokyo and outlying communities, highlighting the need for additional information to define recent slip rates, magnitude, and recurrence of past earthquakes on them.