Disclosed herein is a method of bonding substrates, a microchip, and a method of manufacturing the microchip capable of joining two substrates in a higher adhered state even when at least one of the substrate has a warpage or a roll. A method of bonding a first substrate and a second substrate each of which is made of glass or a resin comprises: a surface activating step for activating each of joining surfaces of the first substrate and the second substrate; and a pressurizing step for pressurizing the first substrate and the second substrate in a state that the first substrate and the second substrate are stacked such that respective joining surfaces contact each other. The joining surface of the first substrate and/or the joining surface of the second substrate are constituted with a plurality of joining regions segmented to be separate from one another by a segmenting recessed portion.