With the growing need for photovoltaic base development in ecologically fragile areas, the construction of county-level ecological sensitivity evaluation model and zoning method is conducive to the "double realization" of the development of renewable energy industry and the goal of ecological environmental protection. Taking Qilian County, Qinghai Province as a case study, This study assesses the impact of photovoltaic base construction on the surrounding ecosystem and develops an ecological sensitivity model based on four factors: terrain conditions, soil conditions, climate conditions, and ecology conditions. Ecological zoning is then performed using the Self-Organizing Feature Mapping (SOFM) network model. The results indicate that: (1) Ecological sensitivity in Qilian County exhibits clear spatial differentiation, driven by the combined effects of terrain, soil, climate, and ecology. The terrain index follows a pattern of mountains > plains, while the soil index is predominantly medium to high. The climate index decreases gradually from northwest to southeast, and the ecological index is mostly low to medium. Under the combined effect of the four factors, the ecological sensitivity index of Qilian County is classified into four levels, and the overall spatial distribution characteristics of "weakening from west to east, and from the center to the north and south." Sensitive areas account for 26.37%, 31.09%, 26.06%, and 16.48% of the proposed photovoltaic area in high, medium, medium-low, and low sensitivity categories, respectively. (2) The SOFM network model is used to divide the proposed photovoltaic base area in Qilian County into four distinct zones. Among them, the western Qilian alpine desert ecologically sensitive area should prioritize ecological protection and restoration, in principle, construction activities unrelated to ecological protection should be prohibited. In the central Qilian upper Heihe River ecological restoration area, moderate photovoltaic development is permitted, provided the ecosystem’s structure and function remain intact. The eastern Qilian alpine shrub energy-ecology coordination area can be combined with shrubs, grasslands and other resources to develop a "photovoltaic +" ecological coordination model. The Southern Qilian Datong River meadow energy-ecology excellent area is a priority site selection area for photovoltaic bases, which can rely on the advantages of regional land resources and ecological resources to adopt a "photovoltaic +" industrial integration approach. The results of this study clearly show the ecological sensitivity distribution pattern of the proposed photovoltaic bases in Qilian County, and the relevant methods can provide a reference for the ecological sensitivity evaluation and zoning of the proposed photovoltaic bases in other counties in the ecologically fragile area.