Although local scale investigation throughout parts of the java island has been conducted to understand about the subsurface condition, there are only a few tomography approaches to prove the previews geological model. In this study we perform ambient noise tomography (ANT) of entire Java Island to delineate subsurface and the relationship between shear wave velocity and basin structure in relation to tectonic influences. Our study utilize data from 114 permanent seismograph stations operated by The Indonesian Meteorological, Climatological, and Geophysical, and Geophysical Agency (BMKG)of continuous seismic record from January–June 2022 (6 month). We obtain more than 6000 potentials of Empirical Green's function and extract the Rayleigh Group Velocity for the period 3 s to 33 s. We perform manual pick for dispersion curves of 6328 of pair cross correlation to correct any artefact. The two step tomography process begins with group wave velocity maps, then we delineate the shear wave velocity structure beneath Java Island from 3 to 30 km from 217 sampling point 1D inversion. Profile Vs ranges from 1.3–4.1 ± 0.1 km/s with low Vs (1.3–2.2 ± 0.1 km/s) interpreted as basins including Bogor, Kendeng and Banyumas basins. On the other hand, the high Vs (2.2–4.1 ± 0.1 km/s) interpreted as crystalline basement or indicate stronger more rigid materials within the crust. The flexural pattern reveals a distinctive characteristic along Java Island, where the basin orientation shows regional variation. In western Java, the flexure trend indicates northward basin development, whereas in eastern Java the flexural axis shifts southward. In central Java, the transition between these two domains suggests a twisting or rotational deformation of the crust, reflecting a complex mechanical response of the Sunda Block to ongoing subduction processes beneath Java.