Formation mechanism of β’’-Mg5Si6 and its PFZ in an Al-Mg-Si-Mn alloy was studied by the means of experiment and first-principles calculations. Results show that at 270°C during the 100 °C/h heating period, β’’-Mg5Si6 precipitated inside the dendrites, whereas precipitation free zones (PFZs) of β’’-Mg5Si6 presented near the dendrite arm regions. The formation of the β’’-Mg5Si6 and its PFZ were related to the concentration of vacancy. Low-concertation zones of vacancy formed near the eutectics during the solidification due to the constitutional supercooling, no β’’-Mg5Si6 precipitated in the low-concertation zones of vacancy due to the vacancy-dependence of β’’-Mg5Si6, the Si vacancy-containing β’’-Mg5Si6 was extremely unstable and Si vacancies prefer to stay away from distribution.