Cu pillar bump (CPB) technology as the representative advanced packaging technology possesses the characteristics of miniaturization and high density, thus playing an important role in the reliability of electronic devices. However, the brittle intermetallic compound (IMC) layer in the joints evidently affects the service performance and reliability of CPB joints. Thus, the influence of IMC layer thickness and microstructure needs to be carefully evaluated. In this study, the reliability of CPB joints with different IMC layer thickness under the condition of isothermal storage and room-temperature electromigration was tested, and the effect of initial IMC thickness of joints on the reliability was revealed. The full-IMC joints have the best isothermal storage reliability while the half-IMC joints perform the worst. Meanwhile, the thin-IMC joints own the best electromigration reliability but the full-IMC joints show the worst because that the initial voids in full-IMC joints accelerate the failure caused by electromigration.