The water–energy–food (W-E-F) nexus approach has become the basis for a host of many methods addressing the security of global resources, whose methods are often nonparametric, due to the complex and indefinable relationship among the three. In this work, the nonparametric evaluation method data envelopment analysis (DEA) is further extended to a three-stage dual-boundary network model (TD-NDEA) for dealing with the “black box” problem in W-E-F Nexus. In the empirical study, the TD-NDEA method is applied to assess the efficiencies of W-E-F nexus in 13 selected cities of Jiangsu Province in China, where W-E-F nexus is innovatively decomposed into three stages, “W-E,” “WE-F,” and “WEF.” External factors such as labor force, urbanization, and economy are included in the assessment. On this basis, environmental governance and policy interventions are utilized as indicators of eco-sustainability to reshape the third stage as “WEF-Eco.” It is perceived from the numeric analysis that (i) regional disparities in the efficiencies of W-E-F nexus expand significantly; (ii) compared with the labor force, urbanization, and economy are more remarkable toward influencing the efficiencies; and (iii) ecological sustainable planning plays an effective role in reducing regional heterogeneity and speeding up the process of regional coordination. Based upon the findings, relevant policy recommendations are carefully designed.
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