Objective The T cell receptor-co-receptor complex (TCR-CD3) plays an important role in the adaptive immune response, and the interaction between its subunits has always been a research hotspot. Due to the limitations of traditional experiments, the study of transmembrane protein TCR-CD3 complexes cannot go deep into the microscopic level.Methods Therefore, we used molecular dynamics simulation methods to analyze the self-assembly mechanism of TCR-CD3 complexes.Results Through coarse-grained simulation (CGMD), we found that the TCR-CD3 complex has an assembly sequence in which αβ sequentially binds δε", γε, and ζζ" during the assembly process, and explained that the α^R253 mutation reduces the interaction between α^K258 and δε".Conclusion We demonstrated that only the transmembrane region of the TCR-CD3 complex is not sufficient to mediate the specific interaction between the subunits of the TCR-CD3 complex. The results of steered dynamics (SMD) and all-atom simulation (AAMD) indicate that the extracellular interaction between ζζ" and the rest of TCR-CD3 is stronger than the transmembrane region. The absence of ζζ" makes the stability of αβδε"γε little change, while the absence of δε" greatly reduces the stability of αβγεζζ".