High-magnesium Portland cement clinker with MgO content of 6% was synthesized with chemical reagent. The effect of cooling method (i.e., furnace cooling, air cooling and liquid-nitrogen quenching) on the mineral composition, C3S crystal type, solid solubility of MgO, and formation of periclase of high-magnesium Portland clinkers with different alumina modulus (IM) (i.e., 0.64, 1.10 and 3.00) was investigated. The samples were characterized by X-ray powder diffraction with Rietveld method, petrographic method and scanning electron microscopy. The results show that a rapid cooling can stabilize C3S crystal into M3 type, and prevent the transformation of C3S crystal from M3 to T3 type. And this has a little effect on the change of IM. The content of C3S is relatively high in the clinker with a low IM and by furnace cooling, and the clinker with a high IM and by liquid-nitrogen quenching. Rapid cooling rate inhibits the crystallization of periclase, and the inhibition effect is more dominant in a low IM clinker. Clinker quenching can keep the morphology of C3S intact, and promote periclase to turn into a fine round granule.