<p>With the increasing demands for the performance of lightweight structural components in fields such as rail transportation and aerospace, the joining of magnesium/aluminum dissimilar alloys has become a research hotspot. However, due to significant differences in physical, chemical, and mechanical properties between magnesium alloys and aluminum alloys, brittle intermetallic compounds are easily formed during the welding process, which severely restricts the improvement of joint performance. In this study, ZK60 magnesium alloy and 6061 aluminum alloy were joined using continuous double-sided friction stir welding. Combined with orthogonal experimental design, thermal–mechanical-fluid multi-physics numerical simulation, and microstructural characterization, the effects of welding parameters on temperature field, stress field, material flow behavior, microstructure evolution, and mechanical properties were systematically investigated. The results indicate that the tool rotation rate is the dominant factor affecting the tensile strength of the joints, and a high rotation rate is beneficial for improving material fluidity and interfacial bonding quality. The ultimate tensile strength of the joint obtained with the optimal parameter set reached 130.8 MPa. A uniform and continuous Al–Mg-Zn ternary compound layer formed at the interface, which effectively suppressed the formation of brittle Al₃Mg₂ and Al₁₂Mg₁₇ phases. Numerical simulation revealed the coupling mechanism between heat input and material flow during the welding process, explaining the differences in microstructure evolution and fracture behavior under different parameters. Grain orientation analysis showed that the deviation of the basal texture on the magnesium alloy side significantly affects the interfacial load-bearing capacity. This study provides a theoretical basis and numerical support for the microstructure control and process optimization of high-performance magnesium/aluminum dissimilar joints.</p> Graphical Abstract <p></p>