With the increase in lightweight components, Al-Si-Cu alloys are extensively applied in the automotive field. In this study, a multi-principal element alloy (MPEA) AlZrNiTi was designed to modify the Al-9Si-3Cu alloy, and the modification effects of individual additions of Zr, Ni, and Ti elements to the alloy were assessed. Moreover, the microstructure evolution, fracture behavior, and the mechanisms of strengthening and toughening during the modification process were investigated. Experimental results showed that when the addition amount of AlZrNiTi alloy was 0.8 wt%, significant refinements were made to the α-Al, eutectic Si, and Al2Cu in the Al-9Si-3Cu alloy, and the mechanical properties were significantly improved. In addition, the AlSiZr phase served as the heterogeneous nucleation core of α-Al was discovered. Furthermore, the AlZiTi phase was enriched at the front edge of the solid-liquid interface in solidification, hindering the growth of α-Al grains. It was also found that Al(Ni, Cu) particles with a size of 336 nm promoted the formation of high-density twins in Si crystal through the impurity-induced twin (IIT) mechanism, thereby modifying the Si phase. Comparative experiments reveal that the modification effect and mechanical properties of AlZrNiTi master adding to Al-9Si-3Cu alloy was obviously better than that of individual adding Zr, Ni, and Ti elements.