In the present work, gravity-magnetic data are utilised to decipher the crustal setup and the thermal regime of the central part of EGMB, which hosts four non-volcanic hot springs: Atri, Tarabalo, Deulajhari, and Taptapani. Regional-scale investigations based on acquired and global gravity and magnetic data have delineated the deeper structural features and their effects on the region's geothermal activities. 3D gravity inversion for Moho depth estimation as well as spectral analysis of magnetic data, Curie point depth (CPD) estimation, and heat flow values due to radiogenic crustal elements provided a better understanding of the variation of thermal structure (e.g., CPD, heat flow, geothermal gradient) with crustal thickness (e.g., Moho surface) and their correlation with the locations of four hot springs in the study area. The observed Curie depth surface below the study area is shallower than the Moho interface obtained from the 3D inversion, resulting in a higher geothermal gradient and higher heat flow estimates due to CPD. Further, surface heat flow due to radiogenic heat production (RHP) of the high-grade metamorphic rocks of the study area is estimated and compared with that obtained from the CPD estimates. Both these estimates are higher than the global mean heat flow value associated with stable continental regions, implying a collective contribution of RHP from lithology of the thin magnetic crust, along with basal heat flux from the deeper part. The major shear zones in the vicinity of the hot springs occur in the region with shallower CPD and higher heat flow, suggesting a possible role played by them and associated fracture/fault networks in transferring the geothermally heated fluid.  Thus, the present study provides a better understanding of the thermal aspects of a portion of the EGMB crust and their consequences for the geothermal setup of the study area.