The work aims to solve the problem of safety risk identification and qualitative analysis during the refrigerated transportation of litchi. Based on factor spaces and fault tree analysis (FTA) model, the relation matrix of risk factors in the refrigerated transportation of litchi was constructed based on the analysis of the security event set, spatial structure (work positions) set and simplified factor set in the refrigerated transportation of litchi. Then, the basic events of accidents in the transportation of litchi under different work positions were obtained by matrix operation. With the calculation results, the fault tree model for the litchi transportation was constructed to obtain the minimal cut sets of fault tree during the transportation. There were 13 minimal cut sets for the refrigerated transportation of litchi, and the structural importance of each basic event was analyzed. According to the research on the structural importance of the minimal cut sets and the events, the security in the refrigerated transportation of litchi is analyzed, and the countermeasures and suggestions on promoting the site safety management are put forward.