Puga–Chumathang geothermal manifestations are located close to the Indus suture zone (ISZ), which acts as the Indo–Eurasia tectonic collision boundary of the NW Himalaya (altitude ~ 4500 m). Hot springs hold significant potential for renewable energy generation and green hydrogen production. Both geothermal fields comprise boiling springs, geysers, and hydrothermal deposits. The structure of the geothermal fields and the key geological factors are hitherto unclear. We propose a new insight into crustal architecture, suggesting a possible connection between the two geothermal fields, based on 3D inversion of magnetotelluric data from a total of 62 sites. The model resolution tests confirm the major conductivity anomalies in the study region. The model highlights the Kaigar Tso fault structure and its role in the geothermal manifestations of Puga valley, and it also recovers a geothermal reservoir model configuration at the Chumathang geothermal region. The prominent conductivity feature (1–10 Ω.m) observed at a depth of ~ 4–8 km can be attributed to a heat source from secondary magma, such as leucogranitic melts derived from the ISZ during the significant Indo–Eurasian collision dynamics. The clue for a common source and a possibility interconnection of these hot springs provides multi-scale geothermal exploration plans in India, aiding the global goal of net-zero carbon emissions.