The paper aims to analyze the consumer joint choice behavior on fresh food purchase channels and terminal delivery services during major public health events, with the purpose of revealing the underlying influencing factors and behavioral characteristics. First, based on random utility maximization theory, the cross-nested logit model is formulated, which takes into account the influence of socioeconomic attribute factors, service attribute factors, risk perception attribute factors and trust perception attribute factors. Second, a questionnaire survey is conducted, and the obtained data are used to estimate the model parameters and perform an elasticity analysis of the utility variables. The parameter estimation results demonstrate that in the context of major public health events, consumers consider adjusting their attitudes toward e-commerce platforms first when the utility variables are altered, and fresh food purchase channels are easily replaced for consumers who choose unmanned equipment home delivery. The elasticity analysis results suggest that consumers are more willing to buy fresh food through community group-buying channels, are more sensitive to the convenience of the purchase process and are less concerned with delivery time. Although person-to-person contact increases the risk of infection, consumers still prefer attended terminal delivery services. Furthermore, consumers least agree with the effectiveness of body temperature detection methods in public places but feel that an effective way to increase consumer trust in enterprises is to strengthen personnel protection measures.