The effect of homogenization treatment on aging behavior of Al3(Sc,Zr) and homogeneity of Mg were studied in an Al-6Mg-0.4Mn-0.15Zr-0.04Sc alloy using Micro-hardness test, optical microscope, scanning electron microscope and transmission electron microscope. The peak hardness of alloy annealing at the normal homogeneous temperature of 475℃ was 83HV, much lower than those isochronally annealed at 175-550℃, demonstrated that the alloy did not obtained the sufficient aging strengthening from Al3(Sc,Zr) particle during one-stage annealing at 475℃. Therefore, two-stage homogeneous treatment was designed. The first stage annealing was selected from 275-350℃, where the 300℃ exhibited the highest peak hardness of 87HV, and the second-stage annealing were performed at 475℃ with the peak hardness of 92HV. The microstructure analyses indicated the Al3(Sc,Zr) particles in two-stage annealing were much finer than that of one step annealing. After annealing at 300℃/7h+475℃/15h, the segregation of Mg disappeared and the Al3(Sc,Zr) particles formed dispersedly at the same time.