Improving the water and land resource system efficiency can effectively alleviate the severe situation of water and land resources in China. Through the two-stage network DEA model, spatial autocorrelation analysis, multiple linear regression, and geographic weighted regression analysis, this paper revealed the change characteristics, distribution types, spatial correlation relationship, and main driving factors of China’s water and land resources system efficiency. The results show that the water and land resources system efficiency fluctuates widely in different regions. Water and land resources systems in nearly half of the provinces belong to the high development, low economic benefit transformation type, mainly distributed in southwestern and northwestern China. The economic benefit transformation is becoming the weak link of water and land resources system. The overall efficiency of water and land resource system has significant spatial positive correlation, and this correlation has an increasing trend. Low-Low Clusters occupy more provinces. The urbanization level, population density, proportion of output value of secondary and tertiary industries, and effective irrigation all have a positive impact on the overall efficiency of water and land resources system. The impact of the proportion of construction land is bidirectional and the per land pesticide application has negative impact in general.