Atomic engineering of complex oxide thin films is now reaching a new paradigm: the possibility to control the cation coordination by oxygen anions. Here, we show two examples of stabilization of novel structural phases by manipulating the oxygen sublattices in complex Cu-based oxide thin films grown on SrTiO3: (i) epitaxial strain stabilization of a near cubic form of CuO and (ii) thickness-dependent structural transformation from bulk planar (polar) to chain-type (nonpolar) in SrCuO2 thin films that relieves the electrostatic instability. Experimental investigation on ultrathin CuO layer identifies the existence of an elongated (c/a ∼ 1.34) rocksalt-type CuO phase, pointing to metastable 6-fold coordinated Cu with the hole occupied in the 3d x 2−y 2 orbital. For ultrathin SrCuO2 layers, we demonstrate the possibility of moving oxygen ion from CuO2-plane to Sr-plane forming chain-type structure. X-ray absorption spectroscopy reveals preferential hole-occupation at the Cu-3d3z 2−r 2 orbital for chain-type structure unlike to the planar case. Our findings testify unique stabilization processes through atomic rearrangement and provide new insight into the experimental realization of novel cuprate-hybrids to look for exciting electronic properties.