The invention relates to the technical field of special-shape aircraft bay connecting section, and particularly discloses a special-shape missile bay section connecting structure for sectional fairing deploying. The special-shape missile bay section connecting structure comprises a guide bay metal shell, a warhead bay metal shell and a bay body adapter ring, wherein the bay body adapter ring is of a step-shaped cylinder structure, and is fixedly connected with the guide bay metal shell through a thread structure, the left cylinder wall of the bay body adapter ring and the guide bay metal shell are fixedly connected through an anti-loosening pin, the warhead bay metal shell is matched with the end surface of the guide bay metal shell, the inner wall of the warhead bay metal shell is matched with the right cylinder wall of the bay body adapter ring, and the warhead bay metal shell and the bay body adapter ring are fixedly connected through a connecting pin. The special-shape missile bay section connecting structure has the advantages that the problems of failure of loosening prevention of bay section large threads and the nonuniform butting surface of the special-shape bay body are solved; compared with the flap type quick connecting, the bearing property of the butting surface is good, the gap of the butting surface is avoided, and the implementation of manufacturing technology is easy.