The non-uniform stiffness distribution of irregular large thin-walled structures leads to warping deformation in the process of machining and assembly. The structure modeling and accurate calculation of the large deformation is the key to predict and control the deviation. A novel irregular higher-order composite shell element based on the absolute nodal coordinate formulation (ANCF) was proposed to accurately calculate the deformation of irregular large thin-walled structures with higher-order slope coordinates and improved shape function, considering the continuity of elements at the contact interface. A discrete method of irregular large thin-walled structures was proposed to solve the problem of node connection and deformation coupling between elements with different thicknesses, and to describe the large deformation of irregular large thin-walled structures effectively by using the combination of irregular higher-order elements and composite elements. An assembly deformation calculation model of irregular large thin-walled structures was proposed based on continuum mechanics. The influence of the thickened area on assembly deviation and stiffness of scalloped segment structures of heavy rocket tank bottom was studied with the new elements and calculation model, so as to provide guidance for structure design.