This paper aims to verify whether the natural resource system of Chongqing, China could support the current development mode of social economy, and measure the current and future sustainability. The 3D Ecological Footprint (EF) model and the ecological sustainability index (ESI) were adopted for the measurement and time series analysis of the per-capita ecological footprint, per-capita ecological capacity, per-capita ecological deficit and depth of ecological footprint (EFdepth) of Chongqing from 2000 to 2017, i.e. the 18 years since the implementation of Western Development Strategy. The authors also calculated the ESI and fitted its future trend. The results show that: From 2000 to 2017, the per-capita ecological footprint, per-capita ecological deficit and EFdepth increased continuously, the ecological capacity remained stable; From 2000 to 2016, the ESI exhibited a declining trend, indicating that the sustainability deteriorated from weakly sustainable to weakly unsustainable; After 2016, the ESI trend changed to gradual increase, and is expected to become weakly sustainable again in 2026, moderately sustainable in 2032, and strongly sustainable in 2037. If the strongly sustainable level is reached early, Chongqing also needs to speed up reforms to optimize the industrial structure, land use, lifestyle and ecologic policies.