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Wafer direct bonding is a generic tool enabling realization of innovative structures. To expand the applications, an ideal bonding method is expect to achieve sufficient bonding strength at room temperature without requiring annealing, low-cost without high-vacuum system and facile treatment process. In this paper, a novel and simple wafer direct bonding process using fluorine containing plasma activation room-temperature bonding is achieved successfully in air ambient. This method is effective for bonding Si to Si wafers. The bonding is very strong even at room temperature with void-free bonding interface. Moreover, it does work well for bonding of silicon and silicon dioxide wafers at room temperature as well. This fluorine containing plasma activated bonding process is able to avoid temperature-related problems as much as possible. It thus can be applied for building heterogeneous structures in 3D integration and sealing of Si-based temperature-sensitive devices in MEMS packaging.