Hydration resistance of synthesized MgO-CaO clinker was improved by surface modification using oleic acid, stearic acid, or complex acids as modifiers, with phosphoric acid as a reference. Unmodified and modified samples were evaluated using a powdering resistance test, weight change test, and flowability test. The remarkable effects of the modifiers on the hydration resistance and flowability of the clinker were manifested, and the complex modifier caused the most significant effect. The mechanism involved the formation of calcium-containing films on the surfaces of the clinker particles, which protected them from hydration. The flowability of the clinker also increased with improved hydration resistance because of the decreased bonded-moisture content. Comparison of infrared spectra between unmodified and modified samples confirmed the formation of surface films.