The present invention provides a purification method of pegylated recombinant human granulocyte colony stimulating factor. The inventor performed extensive researches of a variety of chromatographic methods, and found that high-purity pegylated recombinant human granulocyte colony stimulating factors can be obtained by using desalting chromatography, ion exchange tandem chromatography and desalting chromatography to perform sequential combined purification. The purification process of the present invention makes full use of the characteristics of the target protein in the surface charge and hydrophobicity, firstly uses an anion exchange chromatography column to effectively remove endotoxin and to increase controllability of the process; and makes full use of strong hydrophobicity of the target protein in the second-stage chromatography, realizes tandem chromatography, and combines removal of endotoxin and protein purification into a step. The process can not only effectively remove endotoxin, but also simplify operation steps, save production time, and improve production efficiency. The process is very suitable for large-scale industrial production.