The efficient utilization and optimal allocation of natural capital play an important role in economic development and human well-being. The production process of natural capital is the input and output processing of its ecological resources and the environment. Improving the rural natural capital utilization efficiency (RNCUE) is an important goal of natural capital investment, and the efficient utilization of natural capital is an important factor for the efficient operation of the regional economy and society. This study uses the super slack-based measure (SBM) model based on undesirable outputs to measure the RNCUE, combines the exploratory data analysis method (ESDA) and spatial Markov transfer matrix to analyse the spatiotemporal evolution characteristics of efficiency, and analyses the influencing factors of the change of the RNCUE in Chongqing through a spatial econometric model. The results show that: (1) The RNCUE in Chongqing is still at a low level as a whole and there is a large space for efficiency improvement and efficient operation. There is a certain spatial dependence on the interaction of efficiency between adjacent districts and counties. (2) High-high agglomeration is concentrated in the western area of Chongqing One-hour Economic Circle, and low-low agglomeration is concentrated in Southeast and Northeast Chongqing. The probability of a large change in the RNCUE in consecutive years is small, and it is easy to form the phenomenon of “club convergence” in space. (3) The RNCUE in Chongqing has been affected by rainfall, temperature, NDVI, the per capita GDP, proportion of fixed asset investment, expenditure for agriculture, and proportion of primary industry and rural population. The influencing factors show that the spatial heterogeneity is significant. The RNCUE has a negative correlation with forest coverage and the expenditure for agriculture, is not significantly positive or negative with the proportion of the primary industry and is positively correlated with the rural population density. This study points out that we can improve the RNCUE in Chongqing by optimizing the spatial differentiation control mechanism, clarifying property rights, enhancing liquidity, and strengthening scientific and technological innovation.