Delineation of the ecological protection and restoration zones from a perspective of an integrated ecosystem (including mountains-rivers-forests-farmlands-lakes-grasslands) is the basis for bringing forward a scientific and rationally proposal to protect and restore ecosystems. However, the current delineation is relatively insufficient for the comprehensive consideration of ecological problems, and it does not reflect the concept that mountains-rivers-forests-farmlands-lakes-grasslands are a shared community. In this paper, taking Shaanxi Province as a study region, we selected 8 indicators to systematically diagnose its ecological problems. On this basis, we delineated the ecological protection and restoration zones at small-watershed scale. The results showed that:(1) the average value of ecological restoration index (ERI) of Shaanxi Province in 2015 was 0.39 (the smaller the value was, the more serious ecological issues that needed to be remedied), and the ERIs of different small watersheds ranged from 0.23 to 0.60. In general, the spatial heterogeneity of ERI in Shaanxi Province was obvious, and it tended to decrease from south to north. (2) There were 8 ecological restoration zones, including the eastern part of the Qinling Mountains in southern Shaanxi, the urban areas in the central of the Guanzhong Plain, the Hanjiang River Valley Basin, the central and southern parts of the Loess Plateau in northern Shaanxi, the Qinling Mountains in the southern Shaanxi, the northern part of the Loess Plateau in northern Shaanxi, Guanzhong Plain area, and Daba Mountain area in southern Shaanxi. Soil erosion, vegetation degradation, and insufficient water resources were the main ecological problems in the Loess Plateau, while the ecological environment in Qinba Mountains area was susceptible to extreme precipitation and soil erosion. For the Guanzhong Plain, ecological problems were vegetation degradation, intensive exploitation of mineral resources, and soil erosion.