With the continuous advancement of China's transportation infrastructure, the number and proportion of highway tunnels in expressway construction are increasing year by year. In order to accurately evaluate the quality and safety of highway tunnel engineering, the finite element analysis is used to evaluate the quality of highway tunnel secondary lining structure, the slotting method is used to analyze the working stress of tunnel secondary lining structure, and the load on the secondary lining structure is inversely analyzed combined with the finite element three-dimensional model to evaluate the quality and safety of tunnel secondary lining structure. The test results show that the error rate of working stress of secondary lining structure deduced by combining slotting method and finite element analysis is 2.22%, the average error rate of vertical uniformly distributed load analysis of two lane and three lane highway tunnels is 7.09%, and the average error rate of horizontal lateral pressure coefficient analysis is 16.37%. The numerical errors are within the acceptable accuracy range of actual highway tunnel engineering. Using finite element analysis to analyze the quality and safety of highway tunnel can accurately evaluate the quality and safety of secondary lining structure of tunnel engineering, and provide effective data reference for actual quality evaluation and defect reinforcement of tunnel engineering.