Heterostructure with a symmetry-mismatched interface provides a promising playground for the exploration of emergent phenomena. Herein, we report a systematic investigation on La2/3Sr1/3MnO3/YBaCo2O5+δ
(LSMO/YBCO) grown on SrTiO3, a heterostructure formed by perovskite oxides of different symmetry. A high-resolution lattice image shows the formation of high-quality perovskite LSMO and A-site cation-ordered oxygen-deficient double perovskite YBCO, without any signatures of atomic reconfiguration at the interface. Surprisingly, the YBCO-buffered LSMO exhibits perpendicular magnetic anisotropy (PMA), though bare LSMO film is in-plane anisotropic. The PMA is robust, appearing even when the thickness of YBCO is only one unit cell. The typical anisotropy constant is ∼4 × 106 erg cm−3. X-ray absorption spectroscopy analysis reveals a preferential occupation of the
d
3
z
2
−
r
2
orbital compared with
d
x
2
−
y
2
, which is confirmed by density functional theory calculations. This orbital reconstruction accounts for the PMA. The formation of a covalent bond between Mn and Co caged by different oxygen polyhedrons, an octahedron and a square pyramid, respectively, stabilizes the orbital reconstruction, resulting in anomalous spin orientation.