The present invention discloses a process of using peracetic acid for inhibiting microorganisms on water treatment, comprising a step of allowing an environment contact of elements including: a diluent of acetic acid and a surfactant that contains at least 9 carbon atoms in the carbon chain with concention being 0.001 to 60 times of the acetate acid and water treatment for at least 1 minute, wherein the surfactant containing a carbon chain having at least 9 carbon atoms is able to penetrate hydrophobic substance in the environment to enhance the ability of acetic acid for inhibiting pathogenic microorganisms.本發明揭露以過醋酸進行水處理以抑制微生物的方法,其包含令經稀釋之過醋酸和濃度為該過醋酸的0.001至60倍之包含至少9個碳原子的碳鏈之界面活性劑與進行水處理之水至少1分鐘,其中藉由該包含至少9個碳原子的碳鏈之界面活性劑對環境中疏水性物質的滲透能增強過醋酸抑制病原性微生物。