Substrate heating effects on the microstructure and magnetic properties of MnAlGe films grown on Si/SiO2 substrate by sputtering system were investigated. The MnAlGe film fabricated by low-temperature substrate heating demonstrated amorphous phase and paramagnetic property. The film of c-axis orientation associated with the Cu2Sb-type structure was obtained by sputtering at a substrate heating temperature of 270°C and it exhibited perpendicular magnetic anisotropy. From the magnetization curves measured at room temperature, the uniaxial magnetic anisotropy energy, Ku, was evaluated to be in the order of 106 erg/cm3, which is consistent with the literature, although the heating processing and temperature are slightly different. Microstructural observation indicated that the c-axis oriented grains were isolated in the matrix of the amorphous phase. The film lost the c-axis orientation at elevated substrate heating temperature, resulting in loss of the anisotropic magnetic property.