To provide a method for compensating a joint gap of overlapped surfaces of thick walls and capable of joining the materials with high quality.

This method includes a step for scanning a surface region selected on a shell surface and a flange overlapped surface by a light beam, a step for calculating the joint gap with respect to a space between the surface region selected on the shell surface and the flange overlapped surface of the flange, a step for calculating an amount, a shape and a volume of a filler required to compensate the joint gap and transmitting the result to a filler device, a step for filling the surface region selected on the shell surface with the filler by the filler device, and a step for compensating the space between the overlapped surfaces or the space at the side of the overlapped surface by the filler by positioning the flange overlapped surface on the surface region selected on the shell surface.