The coexistence of ferromagnetic metallic phase and antiferromagnetic insulating phase in nanoscaled inhomogeneous perovskite oxides accounts for the colossal magnetoresistance. Although the model of spin-polarized electron transport across antiphase boundaries has been commonly employed to account for large magnetoresistance (MR) in ferrites, the magnetic anomalies, the two magnetic phases and enhanced molecular moment, are still unresolved. We observed a sizable MR in epitaxial spinel films (NiCo2O4-δ) that is much larger than that commonly observed in spinel ferrites. Detailed analysis reveals that this MR can be attributed to phase separation, in which the perfect ferrimagnetic metallic phase and ferrimagnetic insulating phase coexist. The magnetic insulating phase plays an important role in spin filtering in these phase separated spinel oxides, leading to a sizable MR effect. A spin filtering model based on Zeeman effect and direct tunneling is developed to account for MR of the phase separated films.