As the dividing line between the north and the south of China, it is necessary for the Qinling Mountains to construct a complete set of evaluation and monitoring index system. Its internal driving factors and internal mechanism should be studied to promote the ecological environment protection at a new level, and also to fully grasp the driving mechanism and changes of the water conservation function. In this study, an evaluation index system of water conservation capacity in the Qinling Mountains was proposed based on geoweighted principal component analysis (GWPCA). The spatial dynamic changes of primary and secondary indicators of water conservation capacity in the Qinling Mountains in 2010 were analyzed, and their spatial distribution mechanism were revealed. Based on GWPCA, considering the water conservation effects of meteorological factors, underlying surface factors and social factors, an index system of water conservation capacity in Qinling Mountains containing 10 spatial variables was constructed. According to the results, the water conservation capacity of the Qinling Mountains could be divided into five grades: low, lower, medium, high and higher. The spatial variation rules of water conservation capacity of the Qinling Mountains were revealed, and some suggestions for ecological management were put forward. The results showed that the water conservation capacity in most areas of Qinling Mountains was at high and higher levels, accounting for 66.48% of the whole region. The water conservation capacity in some economic development regions and the central region of Qinling Mountains is at low and low levels. Extreme climate events and human activities were the main reasons for its distribution. The index system of water conservation capacity in Qinling based on this method could effectively quantify the water conservation capacity in Qinling and its spatial heterogeneity, and could clarify the main driving factors.