The paradigms of productivism, post-productivism, and neo-productivism dominated the global agri-food system in turn since 1945, and the current system is still in the making with the trends of industrialization, globalization, corporatization, and transition towards sustainability. For a long time, the impacts the system generated on the environmental, agrarian, and food domains unavoidably lead to the following seven key issues: (1) The contemporary mode of agricultural production is continuously generating environmental impacts, instead of eliminating them； (2) The process of putting the ideology of sustainability into practice is slow and less effective； (3) Although confronting pressures, agriculture is still profoundly influenced by the productivist paradigm; (4) As the modern agri-food sector can hardly be independent of the distant market and the global supply chain, the space for smallholder farmers’ in this sector has been massively narrowed down; (5) The ″food from nowhere″ regime has either apparent or potential impacts on food safety; (6) The quality turn in food consumption has offered market opportunities, and possibly develops new profit space for corporations; however, it could not guarantee food access for all consumers; (7) The privatization of food security is aggravating the vulnerability of agricultural production and the food supply system. The impacts generated from the above issues have weakened the legitimacy of the current system and have also been the driving forces for transformation. However, the lock-in effects generated by the mainstream institutional system have constrained the capability of the system in problem-solving; as a result, the productivist paradigm still dominates the agri-food sector. This research focuses on the lock-in effects concerning the seven issues alongside regime change in the agri-food system, and analyses how the ″lock-in″ happened and what the structural causes were. This research has discussed three lock-in trajectories identified during the transformation, which are: (1) The problem/conflict has become deepened in the process of change, such as agrarian and food security issues； (2)The alternative strategy for problem-solving has been limited or narrowly interpreted, such as environmental issues； (3) The alternative strategy has been conventionalized in terms of its core value and means when incorporated into the mainstream institutional system, such as food safety issues； (4) Based on lessons from the past, we cannot merely rely on systemic adjustment to the systemic problems; as this could even accomplish the very opposite. The evolving process of ″productivist - post-productivist -neo-productivist″ systems shows that the transformation has not successfully tackled the problems encountered at different stages, while deepening the structural conflicts. The existence of the lock-in effects is the consequence of institutional path dependency under neoliberal discourses, which sets up obstacles for system innovation. Given the fact that the current agri-food system is at a crossroads, to break through the lock-in effects and loosen the system for innovation, it is necessary to deepen the understanding of the agri-food system in a reflexive manner, provide protected space for problem solving-oriented novel practices, and ensure useful feedback from niche-regime interactions.