A flange fastening structure includes a first flange made of metal and a second flange made of plastic. Stepped nuts are provided in the second flange and each have a large-diameter portion and a small-diameter portion. The second flange has at least one raised portion on a surface of the second flange facing the large-diameter portion. The at least one raised portion is made of plastic. A height of the at least one raised portion is set such that the at least one raised portion pressed with the large-diameter portion is deformed when the first flange and the second flange are fastened together with bolts and the nuts. The small-diameter portion of each of the nuts contacts the first flange to limit fastening positions of the nuts and the bolts when the first flange and the second flange are fastened together with the bolts and the nuts.