Abstract Geothermal resources are abundant in the southeast urban area of Beijing, but the complex geological structure and high geomagnetic interference in the urban area make it difficult to detect the distribution characteristics of geothermal resources by the electromagnetic exploration method from natural sources. This paper presents an integrated physical exploration method combining the controlled source acoustic magneto-telluric (CSAMT) and gravity exploration for middle-deep geothermal exploration in the southeast Beijing urban area. The method is verified by examining the recommended boreholes, which have produced water at temperatures of 62.5°C and 63°C. This is a highly beneficial and socially impactful outcome, and it serves as a valuable reference for future exploration and utilization of geothermal resources in this area. It also has significant implications for future exploration and utilization of geothermal resources not only in the southeastern urban area of Beijing but also in similar urban environments around the world. The methodologies and findings from this research offer a valuable blueprint for future geothermal energy prospecting and development, contributing to the global transition towards cleaner and more sustainable energy alternatives.