AbstractArtificial perovskite oxide nanostructures possess intriguing magnetic properties due to their tailorable electron–electron interactions, which are extremely sensitive to the oxygen coordination environment. To date, perovskite oxide nanodots with sizes below 50 nm have rarely been reported. Furthermore, the oxygen octahedral distortion and its relation to magnetic properties in perovskite oxide nanodots remain unexplored thus far. Here, the magnetic anisotropy in patterned SrRuO3 (SRO) nanodots as small as 30 nm are studied. The constituent elements, in particular oxygen ions, are directly visualized via performing atomic resolution electron microscopy and spectroscopy. It is observed that the magnetic anisotropy and RuO6 octahedra distortion in SRO nanodots are both nanodot size‐dependent but remain unchanged in the first 3‐unit‐cell interfacial SRO monolayers regardless of the dots’ size. Combined with first principle calculations, a unique structural mechanism behind the nanodots’ size‐dependent magnetic anisotropy in SRO nanodots is unraveled, suggesting that the competition between lattice anisotropy and oxygen octahedral rotation mediates anisotropic exchange interactions in SRO nanodots. These findings demonstrate a new avenue toward tuning magnetic properties of correlated perovskite oxides and imply that patterned nanodots could be a promising playground for engineering emergent functional behaviors.