Due to the depletion of the raw material base and a technogenic materials addition into a raw mix for the Portland cement clinker synthesis, sulfur and its oxides amount in a raw mix increases. According to literature the Portland cement clinker synthesis in the presence of a sulfur oxides significant amount is difficult. As the content of SO3 in the raw mix increases the amount of C2S increases while C3S and C3A amount decrease. With an equal total content of C2S and C3S in the clinker their ratio C3S/C2S decreases with an increased content of SO3. These factors lead to a deterioration in the Portland cement clinker quality. The clinker formation reactions thermodynamic analysis and some experimental studies allow determining reasons for the Portland cement clinker quality deterioration. It was found that the presence significant amount of a SO3 in the raw mix the synthesis in solid phase of low-basic C4A3 S¯ (ye’elimite) is the thermodynamically preferred rather than high-basic C3A and C4AF. As a result, excess and crystallized free lime inhibits the C3S synthesis through the liquid phase. The experimental studies result helped to develop a methodology for calculating the composition of a raw mix from materials with significant amount of SO3. It allows to reduce the SO3 negative effect on the Portland cement clinker synthesis and to obtain high-quality Portland cement.