The invention relates to a mounting system special for accurately machining two supporting holes of an elastic tube assembly and a method. The mounting system special for accurately machining two supporting holes of an elastic tube assembly comprises a workpiece initial mounting mechanism, a rapid searching mechanism and a connecting and equalizing mechanism, wherein the workpiece initial mounting mechanism comprises an initial searching element, a supporting plate and a clamping mechanism and clamps the elastic tube assembly arranged on the searching element; the rapid searching mechanism comprises a searcher, a searching element, a searching characteristic surface matched with the searcher on the workpiece initial mounting mechanism and a pneumatic clamping mechanism, the workpiece initial mounting mechanism is matched with the searcher through the searching characteristic surface and the searching element thereon so as to rapidly and accurately position the whole workpiece/clamp ona machine tool and machine large holes and outer conical surfaces; and then the initial mounting mechanism is taken down to be remounted on the searcher again to machine small holes. By mounting a workpiece outside the machine tool, the invention can greatly improve the mounting efficiency and the reliability of the workpiece and decrease the coaxiality error from 0.04 to 0.02.