The engineering geological characteristics of the Large High Altitude Air Shower Observatory (LHAASO) site were systematically investigated. LHAASO is the world’s highest-altitude and largest ultra-high-energy gamma-ray observatory independently built and operated by China, and the achievement of its scientific objectives depends on the long-term stable operation of three major detector arrays: the Water Cherenkov Detector Array (WCDA), the Kilometer Square Array (KM2A), and the Wide Field-of-view Cherenkov Telescope Array (WFCTA), under an extreme high-altitude environment. However, the site is located in the Daocheng palaeo-ice cap area, where the engineering geological conditions are highly complex. The main engineering geological challenges include regional tectonic stability under the complex seismotectonic setting of the eastern margin of the Qinghai-Tibet Plateau, site utilization and foundation deformation stability under complex glacial-fluvial geological conditions, and seasonally frozen ground at an extremely high altitude. In this study, regional tectonic analysis, detailed micro-geomorphological characterization, drilling, geotechnical testing, and in-situ frost-depth measurements were conducted to identify the engineering geological characteristics of the site. Because WFCTA is movable and imposes relatively weak constraints on site zoning, the coupling analysis focused on WCDA and KM2A. On this basis, a collaborative site utilization method and zoning scheme were proposed by coupling the core foundation requirements of WCDA and KM2A with the engineering properties of different geological units. The results show that this method introduces the differences in detector functional requirements into engineering geological zoning, shifting site evaluation from a single assessment of geological condition quality to an adaptability analysis between engineering requirements and geological conditions. Through the systematic procedure of “requirement interpretation–geological zoning–coupling matching–functional zoning”, this method promotes the matching between geological units and engineering functions and improves the utilization efficiency of limited and complex site resources. The proposed collaborative utilization method provides a methodological reference for the preliminary site investigation of precision scientific facilities in high-altitude and complex geomorphological areas.