Oxygen vacancy configurations and concentration are coupled with the magnetic, electronic and transport properties of perovskite oxides, manipulating the physical properties by tuning vacancy structures of thin films is crucial for applications of many functional devices. In this study, we report a direct atomic resolution observation of preferred orientation of vacancy ordering structure in the epitaxial LaCoO3-x (LCO) thin films under various strains from large compressive to large tensile strain utilizing scanning transmission electron microscopy (STEM). Under compressive strains, the oxygen vacancy ordering prefers to along the planes parallel to the heterointerface. Changing the strains from compressive to tensile, the oxygen vacancy planes turn to be perpendicular to the heterointerface. Aberration-corrected STEM images, electron diffractions, X-ray diffraction (XRD) combined with X-ray photoelectron spectroscopy (XPS) demonstrate that with increasing misfit strains, the vacancy concentration increases, and vacancy distribution is more ordered and homogeneous. The temperature dependent magnetization curves show the Curie temperature increases displaying a positive correlation with the misfit strains. With changing the strain from compressive to tensile, anisotropy fields vary and show large values under tensile strains. It is proposed that oxygen vacancy concentration and preferred ordering planes are responsible for the enhanced magnetic properties of LCO films. Our results have realized a controllable preparation of oxygen vacancy ordering structures via strains, and thus provide an effective method to regulate and optimize the physical properties such as magnetic properties by strain engineering.