Safety assurance is a key challenge in the new stage of tunnel construction in China. The Wulipo Tunnel on the Jiumian Expressway is taken as the engineering background. A long-term safety evaluation technology for layered soft-rock tunnels in complex and difficult mountainous areas was studied. Rock physical and mechanical tests were first conducted. Numerical simulations of 147 working conditions were then performed by using the ubiquitous joint model. The coupled effects of dip angle and strike direction on tunnel deformation and stress under three stress states were revealed. A dip angle and strike direction influence coefficient was defined and quantified. Its evaluation benchmark intervals were also established. A long-term safety evaluation index system for layered rock masses was then constructed through data investigation, field monitoring, and numerical simulation. The dip angle and strike direction influence index was included in this system. A safety evaluation model was established by using DEMATEL-ANP, the improved entropy weight method, a combined weighting method based on the goodness of fit of the normal distribution of sample evaluation result sequences, and the VIKOR method based on vector fluctuation similarity. Subjective and objective weighting were integrated in the model. The limitations of traditional evaluation methods were reduced. The proposed method was validated by a typical section of the Wulipo Tunnel. The evaluation results are in good agreement with the actual field lining defects. The results show that the proposed safety evaluation technology system can accurately reflect the safety state and long-term evolution trend of layered soft-rock tunnels. The system has good engineering applicability and reliability.