Wafer direct bonding is an attractive approach to manufacture future micro-electro-mechanical system (MEMS) and microelectronic and optoelectronic devices. In this paper, a combined hydrophilic activated Si/Si wafer direct bonding process based on wet chemical activation and O2 plasma activation is explored. Additionally, the effect on bonding interface characteristics is comprehensively investigated. The mechanism is proposed to better understand the nature of hydrophilic bonding. The water molecule management is controlled by O2 plasma activation process. According to the contact angle measurement and FTIR spectrum analysis, it can be concluded that water molecules play an important role in the type and density of chemical bonds at the bonding interface, which influence both bonding strength and voids’ characteristics. When annealed at 350 °C, a high bonding strength of more than 18.58 MPa is obtained by tensile pulling test. Cross sectional SEM and TEM images show a defect-free and tightly bonded interface with an amorphous SiOx layer of 3.58 nm. This amorphous SiOx layer will induce an additional energy state, resulting in a lager resistance. These results can facilitate a better understanding of low-temperature hydrophilicity wafer direct bonding and provide possible guidance for achieving good performance of homogenous and heterogenous wafer direct bonding.