Sr2CoRuO6 in its bulk form shows spin glass behavior with a transition temperature of 95 K, and in its epitaxial thin film, it shows similar behavior with a transition temperature of 135 K. We have studied the structural, electronic, and magnetic properties of a polycrystalline thin film of oxygen-deficient Sr2CoRuO6−δ (SCRO), which shows ferrimagnetic or glassy behavior up to room temperature. The presence of oxygen deficiency causes multivalent cations Co3+ and Co2+ and Ru4+ and Ru5+, which introduces various kinds of magnetic interactions between Co3+–O–Co2+, Co3+–O–Ru4+, Co2+–O–Ru4+, Co3+–O–Ru5+, and Co2+–O–Ru5+ exchange paths, producing unusual exchange bias effects in the single layer thin film of SCRO. The interionic charge transfer between Co and Ru ions as a result of the negative charge transfer energy of the system helps in visualizing the unconventional exchange bias effect in the system.