Portland-cement clinker with a SO3 content up to 3.4% was produced in a cement kiln using waste gypsum board, and the influence of SO3 content on the clinker mineral was investigated. Formation of anhydrite (CaSO4) in the clinker with over 1.6%-SO3 was attributed to a thermodynamic effect but not to the residual waste gypsum board. The mineral composition with a higher SO3 content exhibited a similar trend to those found in the previous studies. The measured alite and belite contents in the clinker agreed with the calculated values derived from modified Bogue’s equation which considers the substitution of sulfur and aluminum by silicon in belite. This substitution increased the lattice parameters of belite. The M1 phase in the alite increased with an increase in SO3 content in the clinker. These characteristics of the high-SO3 clinker indicates that the waste gypsum was decomposed stably to clinker minerals in the cement kiln.