Lattice mismatch induced epitaxial strain has been widely used to tune functional properties in complex oxide heterostructures. Apart from the epitaxial strain, a large lattice mismatch also produces other effects including modulations in microstructure and stoichiometry. However, it is challenging to distinguish the impact of these effects from the strain contribution to thin film properties. Here, we use La0.9Sr0.1MnO3 (LSMO), a lightly doped manganite close to the vertical phase boundary, as a model system to demonstrate that both epitaxial strain and cation stoichiometry induced by strain relaxation contribute to functionality tuning. The thinner LSMO films are metallic with a greatly enhanced TC which is 97 K higher than the bulk value. Such anomalies in TC and transport cannot be fully explained by the epitaxial strain alone. Detailed microstructure analysis indicates La deficiency in thinner films and twin domain formation in thicker films. Our results have revealed that both epitaxial strain and strain relaxation induced stoichiometry/microstructure modulations contribute to the modified functional properties in lightly doped manganite perovskite thin films.