A method for preparing low-cost clean steel includes steps of: preliminarily desulfurizing iron melt: preliminarily desulfurizing in an iron melt channel during blast furnace tapping and during iron folding in an iron folding room, adding a desulfurizing ball into the iron melt during the blast furnace tapping or the iron folding; dephosphorizing and controlling sulfur: dephosphorizing and controlling sulfur during converter steelmaking, in such a manner that P≦0.014% and S≦0.004% during tapping; rapidly dephosphorizing by slag-forming: rapidly dephosphorizing by slag-forming during converter tapping, at a converter end point, controlling a C content at 0.02˜0.10%, adding a dephosphorizing ball through an alloy chute during the converter tapping, blowing argon and stirring at the same time; purifying steel melt during RH refining: adding a purifying ball at a late stage of the RH refining when a vacuum degree is at 66.7˜500 Pa; and continuously casting with whole-process protection.