Atom flux is one of the main factors influencing the quality of nano-gratings fabricated by atom lithography. Based on the theoretical model of eruption volume of atomic furnace tube, the atom flux levels for three typical kinds of furnace tubes are compared by the combination of theory and experiment. Moreover, with the best furnace tube configuration, the peak to valley height of the fabricated Cr nano-gratings increases up to 100 nm, which further optimizes the quality of nano-gratings.