We have devised a novel process integration technique aimed at minimizing the recess of Cu pads, successfully achieving ultra-fine 0.4 μm pitch Cu–Cu connections comprising 50,000,000 links with reliable electrical properties. Notably, no bonding voids were observed throughout the process. A correlation analysis between the total resistance and the number of connection scales demonstrated excellent linearity. The contact resistance per connection, representing the slope of the line, was approximately 3.2 Ω. Our developed process integration method effectively enabled the realization of ultra-fine 0.4 μm pitch Cu– Cu connections with minimal resistance. Additionally, we conducted an evaluation to assess the impact of bonding misalignment on electrical properties and reliabilities. Within the range of ±200 nm misalignment, the contact resistance exhibited a gradual increase due to the decrease in the contact area between the upper and lower pads. Furthermore, our findings confirm that the contact resistance remains within +10% of its value up to a misalignment of approximately ±100 nm.