Characterizing the interior structure of the Jakarta Basin, Indonesia, is important for the improvement of seismic hazard assessment there. A dense-portable seismic broad-band network, comprising 96 stations, has been operated between October 2013 and February 2014 covering the city of Jakarta. The seismic network sampled broad-band seismic noise mostly originating from ocean waves and anthropogenic activity. We used horizontal-to-vertical spectral ratio (HVSR) measurements of the ambient seismic noise to estimate fundamental-mode Rayleigh wave ellipticity curves, which were used to infer the seismic velocity structure of the Jakarta Basin. By mapping and modelling the spatial variation of low-frequency (0.124-0.249 Hz) HVSR peaks, this study reveals variations in the depth to the Miocene basement. These variations include a sudden change of basement depth from 500 to 1000m along N-S profile through the centre of the city, with an otherwise gentle increase in basin depth from south to north. Higher frequency (2-4 Hz) HVSR peaks appear to reflect complicated structure in the top 100m of the soil profile, possibly related to the sediment compaction and transitions among different sedimentary sequences. In order to map these velocity profiles of unknown complexity, we employ a trans-dimensional Bayesian framework for the inversion of HVSR curves for 1-D profiles of velocity and density beneath each station. Results show that very low-velocity sediments ( < 240ms-1) up to 100 m in depth cover the city in the northern to central part, where alluvial fan material is deposited. These low seismic velocities and the very thick sediments in the Jakarta Basin will potentially contribute to seismic amplification and basin resonance, especially during giant megathrust earthquakes or large earthquakes with epicentres close to Jakarta. Results have shown good correlationwith previous ambient seismic noise tomography and microtremor studies. We use the 1-D profiles to create a pseudo-3-D model of the basin structure which can be used for earthquake hazard analyses of Jakarta, a megacity in which highly variable construction practices may give rise to high vulnerability. The methodology discussed can be applied to any other populated city situated in a thick sedimentary basin.