In this work, an ultra-thin cobalt film is used as a passivation layer to achieve a Cu–Cu quasi-direct bonding process, and successful bonding was achieved at the bonding temperature of 230 °C with the bonding pressure of 0.5 MPa in non-vacuum conditions. A tensile bonding strength of over 12.8 MPa can be achieved. With the cobalt layer, the total film roughness is greatly reduced to around 1 nm, and the cross-sectional transmission electron microscope images reveal the presence of a void-free bonding interface. Time-of-flight secondary ion mass spectrometry depth analysis is carried out using a PVD deposited multilayer sample, which simulates the bonding process without pressure. It is found that a Cu–Co intermixing layer formed between the Cu and Co interfaces during annealing, and Cu has diffused into the Co layer. Due to the nanocrystalline structure of the Co film and the low roughness of the system, a low bonding temperature can be achieved. These results demonstrate that Co, which can be selectively grown on the Cu surface, can be used as a passivation layer to achieve low-cost and high-quality interconnect for the three-dimensional integrated circuits.