Most observed phase separation phenomena in complex oxides occur in systems with chemical dopants or structural defects, and theories have established the strong connection between phase separation and the random distribution of chemical dopants. Recent experiments on fabricated high-quality oxide superlattices also confirmed that the phase separation is suppressed in the clean systems without chemical disorders. Thus far, phase separation in strongly correlated oxides without the need of chemical dopants or structural defects has not been fully demonstrated. Here, we have built chemically ordered hybrid superlattices using prototypical SrRuO3 and SrTiO3 perovskite oxides. Contrary to previous understandings, we observe phase separation of two magnetic phases with different spin easy axes. We elucidate this phenomenon through first-principles calculations that the hybrid superlattices have a spontaneous structural instability, leading to a coexistence of ferromagnetic and antiferromagnetic phases. Our findings provide an alternative pathway other than chemical doping to introduce phase separation in correlated oxides and imply that phase separation can exist in clean systems without the need of chemical disorders.