The invention provides an accurate assembly welding method for a butt joint flange plate with an ellipsoid ball box bottom in a whole bottom state. The method includes the following steps that a hole opening center and an assembly contour line of a flange hole welding area of a to-be-welded flange are measured and marked off; oxidized films at the box bottom and on the inner and outer surfaces of the to-be-welded area of the flange are removed; the box bottom position is fixed in an inner expanding and outer pressing method, so that a supporting center normal of an inner-supporting supporting piece and the normal of the hole opening center can coincide with the axis of a milling cutter; machining of a flange hole is completed in a process method that rough milling is performed first and then finish milling is performed; the flange plate is installed and checked, and interference assembly is adopted as an assembly mode; a welding track is demonstrated; and a welding process of single-face double-layer suspended variable polarity TIG welding of positioning, bottoming and face covering is adopted to weld the flange plate and the box bottom. By means of the accurate assembly welding method, numerical control automation of assembly and hole opening can be achieved, the welding track and the welding heat input are accurately controlled, the welding deformation is reduced, and the welding quality and the size precision of the flange plate are improved.