With etching rates of argon ion milling greatly reduced, the conventional fabrication process of mesa-structured intrinsic Josephson junctions is improved by precisely controlling and measuring the parameters of the fabrication, which include the thickness of metal layers and the time and etching rates of argon ion milling. We have obtained intrinsic Josephson junctions of mesa structure, in which the number of junctions ranges from 3 to 12 and is controllable with the error within ±1. The thickness of the Bi 2 Sr 2 CaCu 2 O 8+ x layer damaged by the etching process is about 2.7 nm, which also contributes to the junction number in intrinsic Josephson junctions. The critical current of each junction in the intrinsic Josephson junctions is consistent except for a surface junction, which shows a nonlinear resistance in the current–voltage ( I–V ) curves. With the fabrication of two top electrodes on the mesa and four-probe measurement, the surface junction is eliminated and the standard supercurrent is registered in the I–V curves.