The invention discloses a novel method for preparing penicillin G sulfoxide, which comprises the following steps: a, selecting a 60000-120000 mu / g penicillin G fermentation solution, and dropwisely adding peroxyacetic acid to obtain a solution I; b, filtering the solution I to obtain a filtrate, and concentrating the filtrate through a nanofiltration membrane of which the molecular weight cut-off is 200-800Da, thus obtaining a concentrated solution; c, regulating the pH value of the concentrated solution with sulfuric acid, and filtering to obtain a penicillin G sulfoxide crude product; and d, dissolving the penicillin G sulfoxide crude product in a methanol water solution, recrystallizing, then cooling to 0-10 DEG C, filtering, washing the obtained crystals with methanol, swabbing off, and performing microwave drying on the obtained product to obtain the penicillin G sulfoxide. According to the invention, the method is simple, the process period is short, and extraction treatment can be performed without using a large amount of organic solvent. Thus, the method disclosed by the invention is low in cost and environment-friendly.