Silicon-direct wafer bonding is a promising technology for manufacturing three-dimensional complex MEMS structures as well as SOI substrates. Amongst the various contributors to the bond quality, surface roughness at nanoscale plays a vital role. However, the effect of surface roughness on direct-bond quality has not been quantified. We conducted bonding experiments on silicon wafers with various surface roughness generated by chemical treatment. The bond quality was evaluated by measurement of the bonding energy. The surface roughness investigated by atomic force microscopy was directly correlated to the bond quality for the first time by means of the bearing ratio, which represents the ratio of the surface area lying above a given depth. The bearing ratio discussed herein is an appropriate criterion for the surface quality of silicon wafers to be direct-bonded.