A substrate bonding apparatus includes a vacuum chamber, a surface activation part for activating respective bonding surfaces of a first substrate and a second substrate, and stage moving mechanisms for bringing the two bonding surfaces into contact with each other, to thereby bond the substrates. In order to activate the bonding surfaces in the vacuum chamber, the bonding surfaces are irradiated with a particle beam for activating the bonding surfaces, and concurrently the bonding surfaces are also irradiated with silicon particles. It is thereby possible to increase the bonding strength of the substrates.