The cement industry has achieved stable usage of waste gypsum board in clinker production. However, few studies have focused on the heat of hydration and physical properties of cements with high-SO3 clinker with different C3A and gypsum contents. Clinker with different amounts of SO3 and coexisting C3A was prepared in an electric furnace. Cement samples were then prepared by adding gypsum. Increasing the clinker SO3 content accelerated the alite reaction and caused aluminate hydrate reaction to occur later. Compressive strength at 3 days increased with SO3 content whereas that after 28 days decreased. The drying shrinkage strain of mortar decreased with increasing SO3 content of the clinker and gypsum at each C3A content. The decrease of drying shrinkage attributed to SO3 in the clinker was smaller than that caused by gypsum SO3. As the clinker SO3 content increases, cement physical properties can be maintained by adjusting the gypsum content.