As a tool of natural capital accounting, ecological footprint models have been used to quantitatively estimate a region's sustainability. Three-dimensional ecological footprint is a new approach in the field of natural capital accounting around the world. Given the modern background of the Belt and Road initiative, the construction of ecological civilization, and the development of the western regions of China, it is significant for the Guanzhong region—an important area on the Silk Road—to choose a sustainable development path in the future. Based on the revised three-dimensional ecological footprint model, this study used three scales including product, land use type, and region to quantitatively calculate the land use ecological footprint size and footprint depth of the Guanzhong region and its respective municipalities from 1995 to 2015. Moreover, Gini coefficient of footprint size and other indicators were added to more clearly analyze the occupancy of natural capital flows and the consumption of natural capital stocks in the study area. Lastly, it evaluated the sustainability of natural capital use of the Guanzhong region and its municipalities. The main conclusions of the study are as follows: 1) From 1995 to 2015, the land use ecological footprint of the Guanzhong region showed a trend of increasing first and then decreasing. The land carrying capacity decreased year by year and the ecological deficit increased year by year, which is not conducive to the sustainable development of the region. 2) The five large cities in the Guanzhong region were in the situation of ecological deficit, and their footprint depth were all more than 1. Consuming stock capital to make up for the shortage of flow capital has become a normal social development pattern in the region. 3) Cropland and construction land were the main land use types occupied by natural capital flows, while grassland, cropland, and construction land were the main land use types of natural capital stocks. 4) Inequality of natural capital flow occupation in the region was gradually increasing. If no reasonable measures are taken, it will reach a relatively unbalanced state in 2025 and a highly unbalanced state in 2030. This study focused on the "actual footprint", comprehensively revealed the land use benefits in the Guanzhong region, and provided a scientific reference for the sustainable development of the region.