Epitaxial La(3/4)Ca(1/4)MnO3/MgO(100) (LCMO) thin film shows an unusual rhombohedral (R-3c) structure with a new perovskite superstructure at room temperature due to the CE-type ordering of La and Ca with modulation vector q=1/4[011]. A-site ordered film was found to be electronically homogeneous down to the 1 nm scale as revealed by scanning tunnelling microscopy/spectroscopy. In contrast, orthorhombic and A-site disordered LCMO demonstrate a mesoscopic phase separation far below the Curie temperature (TC). Unique La/Ca ordering compensates the cation mismatch stress within one supercell, a(S) approximately 1.55 nm, and enhances the electronic homogeneity. The phase separation does not seem to be a unique mechanism for the colossal magnetoresistance (CMR) as very large CMR approximately 500% was also observed in A-site ordered films.