Nanhong agate, esteemed for its vivid color and natural shine, is experiencing a scarcity in supply despite its high demand. The primary deposits of agate, typically found near the surface, have not been extensively explored due to the predominance of traditional manual excavation methods. This research examined the Nanhong agate deposits in the Zhaojue–Meigu region of Liangshan, China, employing the integration of geological and geophysical surveys. Field geological surveys allowed us to outline the general areas where agate is found. Following this, using magnetic surveys, vertical electrical sounding, and controlled-source audio magnetotellurics, agate deposits were located within the conglomerate layer of the second member of the Feixianguan Formation from the Lower Triassic period at depths of less than 100 m. Our results identify mineralized layers, Xuanwei Formation mudstone, and the underlying bedrock, thus supporting the creation of a mineral prediction map. This research provides essential insights and guidance for agate exploration and the development of associated mineral resources.