The invention relates to a method for extracting plasmids with endotoxin removed on a large scale. The method comprises the steps of acquiring roughly-separated plasmid DNA by virtue of a classical alkaline lysis method, sequentially adding isopropanol, an NH4Ac solution, RNase A and NaCl, adding a mixed solution of PEG6000 and NaCl, dissolving and precipitating by virtue of a TE solution, repeatedly precipitating by virtue of absolute ethyl alcohol, washing and precipitating by virtue of 70% alcohol, simultaneously coordinating with centrifugation, drying, and finally dissolving and precipitating by virtue of the TE solution, so as to obtain target plasmids. According to the method, the pollution caused by endotoxin to plasmid DNA can be well removed, all reagents are standing chemical reagents in a laboratory, and the operation method is simple, easy to control and suitable for large-scale extraction of plasmids. The concentration of the plasmids can reach 5mg/mL, the endotoxin is lower than 5EU/mu g, and the plasmids can be applied to digestion, DNA sequencing, cell transfection, virus packaging and clinic animal immunization experiments.