Analyzing the traffic capacity of extra-long tunnels is crucial in assessing their sustainable capacity. However, previous studies on tunnel capacity mainly considered the influence of a single factor, ignoring the interaction between multiple factors, which cannot reflect the actual tunnel capacity. Therefore, considering the influence of multiple factors, this paper constructs an actual capacity calculation model for extra-long tunnels. Firstly, by combining hierarchical analysis and the entropy method, we determined the key factors that influence the capacity of extra-long tunnels. Secondly, based on the constructed traffic simulation model, we constructed an actual capacity model of extra-long tunnels by using multiple non-linear regression equations and tested the goodness of fit with the help of the misfit term. Finally, we determined the key correction coefficients of the model using the difference proportion method. Taking Qingdao Jiaozhou Bay undersea Tunnel as an example, the research results show that the method proposed in this paper can accurately determine the tunnel capacity with an error of less than 4%, providing a theoretical basis and practical guidance for the management and control of the tunnel’s sustainable carrying capacity after traffic congestion.