The invention discloses an eccentric connecting pipe flange deformation preventing tool and a using method thereof, belongs to the field of large container manufacturing, and overcomes the defects inthe prior art. The eccentric connecting pipe flange deformation preventing tool structurally comprises supporting pipe assemblies, right-angle connecting plate assemblies and connecting plates, wherein the number of the supporting pipe assemblies is three, and the three supporting pipe assemblies comprise one large supporting pipe assembly in the vertical direction and two small supporting pipe assemblies in the transverse direction; the number of the right-angle connecting plate assemblies is two; the number of the connecting plates is two, and the connecting plates are correspondingly connected with two eccentric connecting pipe flanges; meanwhile, the eccentric connecting pipe flanges are connected with the large supporting pipe assembly through the two small supporting pipe assembliesand the right-angled connecting plate assemblies. The using method comprises the steps that the two connecting plates are correspondingly fastened with the two eccentric connecting pipe flanges; the two small supporting pipe assemblies and the two right-angled connecting plate assemblies are correspondingly installed; the lengths of the two small supporting pipe assemblies and the large supportingpipe assembly can be adjusted by rotating adjusting bolts; the whole device is fixed after all lengths and distances meet the requirements; and the two eccentric connecting pipe flanges are assembledto be welded and fixed to an equipment shell. According to the tool, the problems that control over size precision of the two eccentric connecting pipe flanges is difficult and welding deformation occurs are solved; and the tool can be repeatedly used.