Room temperature hybrid bonding is a good candidate to replace thermal compression bonding due to its better resistance to Cu oxidation and its capability for large die integration. However, the bonding mechanism with Cu thickness non-uniformity and real dishing conditions has not yet been fully understood. To study the mechanism and to explore the window of annealing temperature for the void-free interface, finite element analysis (FEA) and auxiliary experiments with real process issues have been conducted. A Cu thickness variation of 6.6% across the whole wafer after electroplating causes a metal dishing between 4 and 16 nm during chemical mechanical planarization. The critical stress (78.1 MPa) of dielectric material gives the upper boundary of temperature, and the complete contact of metal limits the lower boundary for our FEA models. The window for the annealing temperature is then simulated to be within a range between 295 °C and 302 °C. This is the first time that FEA with a non-uniform process input has been implemented to generate a process window of die-to-wafer (D2W) hybrid bonding for real world application. This paper provides a deep understanding and practical guidance for D2W hybrid bonding.