C-axis oriented La0.7Sr0.3MnO3.δ (LSMO) films were fabricated on the top of SrTiO3/YBa2Cu3O7 grown on MgO(001) substrates. From x-ray φ-scan and planar transmission electron microscopy measurements, the LSMO layer in the LSMO/SrTiO3/YBa2Cu3O7/MgO heterostructure is found to have coherent in-plane grain boundaries with a predominance of 45° rotations (between  and  grains) in addition to the cube-on-cube epitaxial relationship. Also, epitaxial LSMO/Bi4Ti3O12/LaAl03 (001) and c-axis textured LSMO/Bi4Ti3O12/SiO2/Si(001) with random in-plane grain boundaries are introduced as the counterparts for comparison. The resistivity and magnetoresistance (MR) of LSMO layer were measured and compared in these three different heterostructures. The low field MR at low temperature shows a dramatic dependence on the nature of the grain boundary. An attempt is made to interpret these results on the basis of correlation between the magnetic properties and grain structures.