A method of manufacturing a bonded body of a semiconductor substrate and a semiconductor device to be mounted on the semiconductor substrate are provided. The method includes: preparing a first base member and a second base member; imparting liquid repellency for a liquid material to at least a part of a bonding film non-formation region of the first base member to form a liquid repellent region thereon; supplying the liquid material onto the first base member to selectively form a liquid coating on a bonding film formation region of the first base member; drying the liquid coating to obtain a bonding film on the bonding film formation region; and bonding the first base member and the second base member together through the bonding film due to a bonding property developed in a vicinity of a surface of the bonding film to thereby obtain the bonded body.