Rapid urbanization poses great challenges to water-energy-food nexus (WEF-Nexus) system, calling for integrative resources governance to improve the synergies between subsystems that constitute the Nexus. This paper explores the synergies within the WEF-Nexus in Shenzhen city while using the synergetic model. We first identify the order parameters and their causal paths in three subsystems and set several eigenvectors under each parameter. Secondly, a synergetic model is developed to calculate the synergy degree among parameters, and the synergetic networks are then further constructed. Centrality analysis on the synergetic networks reveals that the centralities of food subsystem perform the highest level while the water subsystem at the lowest level. Finally, we put forward some policy implications for cross-sectoral resources governance by embedding the synergy degree into causal paths. The results show that the synergies of the Nexus system in Shenzhen can be maximized by stabilizing water supply, coordinating the energy imports and exports, and reducing the crops sown areas.