In this paper, the hydrophobic plasma-activated bonding of GaAs/Si was studied. We systematically analyzed the effect of different power, gas flow rate and activation time of plasma to the roughness of GaAs and Si wafers. The roughness of GaAs wafers decreased with increasing of power and activation time of plasma. The roughness of Si wafers did not change significantly with increasing of power of plasma, and decreased first and then increased with increasing of gas flow rate of Ar in our experiment. The number of dangling bonds in the surface of GaAs and Si wafers was increasing with the activation time. When the activation time was 3 minutes, the GaAs/Si wafers were successfully bonded under different power of plasma. By scanning acoustic microscope (SAM) testing, it was found that when the power was 200W, the bonded GaAs/Si wafer had the best bonding interface. Furthermore, the GaAs/Si bonding internal mechanism by plasma-activated bonding method was analyzed by testing the chemical composition of the bonding interface.