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Transmissible gastroenteritis virus (TGEV), as a severe virus and causes a high mortality in piglets, has threatened and given large economic losses for swine industry globally. There is an urgent to develop an effective subunit vaccine against TGEV to control the spread of the disease. Viral antigens, spike glycoprotein (S), is one of the most ideal antigenic components for vaccine design. In this study, we used immunoinformatic approaches, together with molecular dynamics analysis, to predict the dominant non-toxicity and high antigenicity Th, CTL, and B cell epitopes derived from S protein and design a multi-epitope subunit vaccine. The results show that the designed TGEV vaccine was non-toxicity, high immunogenicity, stable, and cost-effective. The molecular docking and dynamic simulations reveal that the designed vaccine has the stable interaction with TLR4. Importantly, the immune simulation results demonstrate that the vaccine can trigger a robust humoral and cellular immune responses, resulting in high titers of IgG and IgM, as well as high levels of interleukins and cytokines (IFN-γ and IL-2). Our findings provide rational design principles for designing a safe and effective subunit vaccine against TGEV as well as a new theoretical basis and strategy for preventing associated CoVs infections.