This study presents the synthesis of high-density aligned wurtzite ZnO nanostructures using thermal evaporation on perovskite (La,Sr)MnO3(LSMO) epitaxy to form a heterostructure without the assistance of metallic catalysis. LSMO epitaxial films are RF-sputtered with various crystal qualities to examine the correlation between the interface and electrical characteristics of the heterostructures. The ZnO nanostructures-LSMO epitaxial heterostructures show electrical rectifying behavior without inserting an ultrathin insulating layer at the hetero-interface. Misfit strain, intrinsic strain, and crystal defects are major factors in causing a phase separation in the as-prepared manganite LSMO epitaxial films. The coexistence of a charge-ordered insulating domain and a ferromagnetic metallic domain causes inhomogeneous electrical contact at the ZnO-LSMO heterointerfaces, further deteriorating the junction characteristics. A high-temperature annealing procedure and moderate LSMO epitaxy film thickness are required for the construction of an efficient ZnO nanostructures-LSMO epitaxy junction.