Co50Pt50 and Co50Pd50 (at. %) alloy thin films are deposited on MgO(111) single-crystal substrates using an ultra-high vacuum radio-frequency magnetron sputtering system by varying the substrate temperature from room temperature (RT) to 600 °C. The film growth, the film structure, and the magnetic properties are investigated. CoPt epitaxial films with the close-packed plane parallel to the substrate surface are obtained for the investigated substrate temperatures. Ordered phase formation is recognized for CoPt films prepared below 400 °C. As the substrate temperature increases from RT to 300 °C, the degree of order increases from 0.05 to 0.30. With further increasing the substrate temperature, the degree of order decreases. From the view-points of degree of order and atomic stacking sequence of close-packed plane, the crystal structure is determined to vary A3(Bh)+A1(L11)→L11→A1 with increasing the substrate temperature. On the contrary, CoPd films epitaxially grow above 200 °C, whereas amorphous films are formed below the temperature. No ordered phases are observed for the CoPd films. The crystal structure is determined to be A1 for the CoPd epitaxial films. The lattice strains of these CoPt and CoPd epitaxial films decrease with increasing the substrate temperature. The CoPt epitaxial films with Bh+L11 and L11 structures show perpendicular magnetic anisotropies. The magnetic properties are influenced by the crystal structure and the degree of order.