The security of water, food and energy is a prerequisite for the 2030 Sustainability Development Goals of the United Nations. The increasing constraints and conflicts worldwide caused by water scarcity, energy shortages and food insufficiency have forced us to reflect on the security of each element and their interconnections. In the past, the main body of research had divisions between each independent resource element or built interlinkages between dual elements (e.g., water-food, water-energy and food-energy). There was insufficient research that regarded the three elements as one system. Thus, a ternary nexus system still needs to be explored. To improve the understanding of the nexus and facilitate ternary synergic management, the present study performed a bibliometric analysis of the literature related to the water-food-energy nexus over a long time range from 1995 to 2018 and applied the CiteSpace technique for visualization. Based on this, we introduced the history and present state of the relevant research. We found that the water scientist community seemed to be relatively more active than other communities for the nexus research. The development tended to be more interdisciplinary from 2010 to 2016. However, nexus research has not yet become a stable and independent discipline and still suffers from large uncertainty in terms of the mechanism and driving forces of multisystem interactions. We categorized the current nexus research into strong or weak nexus, and illustrated that water, food and energy were inextricably interlinked as inputs or outputs for one another and that the existing close interlinkages (both economically and technologically) formed cross-sector/region cascading effects as one integrated system with a shared future for food, water and energy. These cascading effects indicate important interlinkages of the nexus system; nevertheless, they are still not well studied. Although there is still high uncertainty for future research, future nexus studies should focus on the research scopes, influencing factors and environmental impacts; building a research framework; or exploring the mechanism and driving forces of multielement interactions. The adoption of an ensemble strategy could help make a tradeoff beyond the stereotype of the current single sector regulation and the separation between sectors and could improve the nexus efficiency through conflict coordination and synergy promotion. In sum, highlights of this study are illustrated below: (1) A nexus thinking is required because the increasing conflicts caused by water scarcity, energy shortage and food insufficiency worldwide are forcing us to re-examine the securities of water, energy and food as well as their interlinkages. (2) We propose that nexus research needs to treat the three systems (water, food and energy) as one system (or “system of systems”). This became a new sustainable security perception beyond the stereotype of efficiency research within a single system. It stressed multi-sector and counterintuitive effects. (3) We suggest that a research framework or theoretical consensus should be developed or clarified in terms of the research scope, determinants and ecological (and environmental) impacts of the nexus system. In particular, urban nexus analysis should be explored. (4) We summarized and identified representative determinants of the nexus system. Climate change and international trade were the first two determinants of significance. Finally, the nexus system research of three systems was bound to be mixed together based on dual interactions. In the future, synthesis and tradeoffs of the water, food and energy should be more systematically analyzed to gain in-depth insights into sustainable development.