In order to include the physical deformation of the large thin-walled structure in the subassembly simulation process in aerospace, a new method based on model reconstruction was proposed. Firstly, finite element method is applied for calculating the deformation of the structural parts according to different assembly status with certain temperature and stress field. Based on the actual deformation data of the surface, some reference point was selected and the method of bicubic B-spline surface interpolation is selected to reconstruct the above surface, and to express the deformed structural parts. Based on physical deformation, a compensating method is proposed to amend assembly path in corresponding assembly process with the constructed model. Under the DELMIA virtual environment with the real, the simulation method has been put in to use on aircraft sidewall panel assembly, and the validity of the method is verified experimentally.