Scientists believed the outbreak of COVID-19 could be linked to the consumption of wild animals, so food safety and hygiene have become the top concerns of the public. An agri-food traceability system becomes very important in this context because it can help the government to trace back the entire production and delivery process in case of food safety concerns. The traceability system is a complicated digitalized system because it integrates information and logistics systems. Previous studies used the technology acceptance model (TAM), information systems (IS) success model, expectation confirmation model (ECM), or extended model to explain the continuance intention of traceability system users. Very little literature can be found integrating two different models to explain user intention, not to mention comparing three models in one research context. This study proposed the technology acceptance model (TAM), technology acceptance model-information systems (TAM-IS) success, and technology acceptance model-expectation confirmation model (TAM-ECM) integrated models to evaluate the most appropriate model to explain agri-food traceability system during the COVID-19 pandemic. A questionnaire was designed based on a literature review, and 197 agri-food traceability system users were sampled. The collected data were analyzed by partial least square (PLS) to understand the explanatory power and the differences between the three models. The results showed that: (1) the TAM model has a fair explanatory power of continuance intention (62.2%), but was recommended for its’ simplicity; (2) the TAM-IS success integrated model had the best predictive power of 78.3%; and (3) the system providers should raise users’ confirmation level, so their continuance intention could be reinforced through mediators, perceived value, and satisfaction. The above findings help to understand agri-food traceability system user intention, and provide theoretical and practical implications for system providers to refine their system design.