The evolution of lattice strain on crystallographic domain structures and magnetic properties of epitaxial low-bandwidth manganite Gd_0.6Ca_0.4MnO₃ (GCMO) films have been studied with films on different substrates: SrTiO₃, (LaAlO₃)_0.3(Sr₂AlTaO₆)_0.7, SrLaAlO₃, and MgO. The X-ray diffraction data reveals that all of the films, except the films on MgO, are epitaxial and have an orthorhombic structure. Cross-sectional dependent microstructural defects. Large-enough tensile strain can increase oxygen vacancies concentration near the interface and can induce vacancies in the substrate. In addition, a second phase was observed in the films with tensile strain. However, compressive strain causes dislocations in the interface and a mosaic domain structure. On the other hand, the magnetic properties of the films, including saturation magnetization, coercive field, and transport property depend systematically on the substrate-induced strain. Based on these results, the choice of appropriate substrate is an important key to obtaining high-quality GCMO film, which can affect the functionality of potential device applications.