The invention discloses a reservoir area anti-seepage geomembrane seepage overhauling device and an overhauling method thereof, and belongs to the field of hydraulic structure engineering applicationstudy. According to the reservoir area anti-seepage geomembrane seepage overhauling device and the overhauling method thereof, concrete anti-seepage walls are adopted to divide the bottom (the lower portion of an anti-seepage geomembrane) of the whole reservoir area into a plurality of small-area independent areas, a drainage blind ditch is arranged below the anti-seepage geomembrane of each areaand connected with a drainage pipe, and the drainage pipes are connected to flow monitoring equipment arranged outside the reservoir area; and after water storage of a reservoir, the water flow changes of the drainage pipes corresponding to the different independent areas in the reservoir can be observed to accurately judge the area where the anti-seepage geomembrane seeps, and accordingly the accurate geomembrane positioning and overhauling function can be achieved. By means of the reservoir area anti-seepage geomembrane seepage overhauling device and the overhauling method thereof, the waterseepage area after water accumulation can be accurately found, water is drained to the water seepage elevation position for repairing, accordingly, the anti-seepage geomembrane can be repaired, wastecaused by excessive water drainage can be avoided, the water seepage position can be accurately found without mistakes, and the water resource, capital and manpower are saved.