Understanding the deep structural controls on reservoir distribution and overburden heterogeneity is important for near-field exploration and green-field development of the Miocene to Holocene carbonate buildups in Central Luconia province in offshore northwest Borneo, Malaysia. Data from 59 stations along an approximately 180 km long controlled-source electromagnetic (CSEM) and magnetotelluric (MT) survey line with three segments recorded using different CSEM transmitter-towing directions were available. We applied three-dimensional (3D) anisotropic resistivity inversion with cross-gradient constraint and verified the resulting models using resistivity logs from nearby wells and the acoustic basement interpreted from seismic data. Our anisotropic resistivity models reveal a fragmented carbonate-rich zone atop a segmented basement comprising electrically resistive horsts coinciding with the northerly Mega-platform, Central and Southern Field Highs, separated by steep conductive zones coinciding with the West, East, and Southeast Troughs previously interpreted from seismic data. The structural highs correlate with the spatial distribution of the known carbonate buildups implying a genetic link. The carbonate bodies are overlain and underlain by persistent layers (C2 and C3) of low resistivity and high anisotropy, which we interpret as indicating compressional deformation or detachment zones. Overburden layer C2 (whose base coincides with the top of a key sedimentary package, Cycle V in seismic data) is thinnest over the East Trough and is discontinuous at the eastern margin of the West Trough, which are locations where drilled wells did not find hydrocarbons implying that the seal rocks are inefficient or breached at those localities. We used these observations to refine the existing seismic-based interpretation of carbonate play-types along our transect indicating how 3D joint CSEM-MT imaging can potentially contribute to derisking or optimizing future exploration and/or development work in this province.