0.4%Mn element was added into 7A99 alloy by semi-continuous casting in the study. TEM, HRTEM and 3DAP were employed to study the microscopic configuration distribution of Mn element in the cast, homogenization and solution aging of 7A99 alloy. The result shows that Mn element in 7A99 aluminum alloy ingot mainly exists in the form of fishbone shape MgZn₂non-equilibrium eutectic compound containing AlZnMgCuMn at grain boundary. After homogenization treatment, Mn element in 7A99 alloy mainly exists in the form of Al₆Mn phase and intermittent, fine, granular S(Al₂CuMg) second phase containing AlZnMgCuMn at grain boundary. A small part of Al₆Mn precipitated phase is dissolved back to the matrix, so that the size range of residual Al₆Mn precipitated phase is 0.2~1μm in the process of solid solution treatment. Mn element always exists in the form of Al₆Mn precipitated phase which is stable in size and non-coherent with aluminum matrix in the aging process of 120℃. Mn element does not precipitate other new phase during the aging proceed and affect the aging precipitation process of Zn, Mg in 7A99 alloy.