The invention relates to a water-rich sandy cobble ground heteromorphosis deep shaft structural system and a construction method thereof. A conventional rectangular shaft section pattern or a circular shaft section pattern, influenced by established subway lines and surrounding environments, can be limited by site conditions and the surrounding environments, so that an operating space does not exist. The water-rich sandy cobble ground allotypical deep shaft structure comprises a heteromorphosis deep shaft structure, wherein the heteromorphosis deep shaft structure comprises a triangular fracture surface shaft structure, an extended digging section heteromorphosis shaft structure and a quadrilateral fracture shaft structure which are arranged from top to bottom; the horizontal section of the triangular fracture surface shaft structure is triangular, and the horizontal section of the upper part of the triangular fracture surface shaft structure is the same as that of the lower part of the triangular fracture surface shaft structure; the horizontal section of the quadrilateral fracture shaft structure is quadrilateral, and the horizontal section of the upper part of the quadrilateral fracture surface shaft structure is the same as that of the lower part of the quadrilateral fracture surface shaft structure; the triangular fracture surface shaft structure is expanded to form the quadrilateral fracture shaft structure through the transition of the extended digging section allotype shaft structure. The water-rich sandy cobble ground allotypical deep shaft structural system disclosed by the invention has the characteristics of being small in occupied area, large in inner space, flexible to convert and capable of being adapted to various environmental requirements, the requirements for small upper part and large lower part are met, and besides, the surrounding environments can be adapted.