The invention discloses a method for finishing cotton yarn with antibacterial organosilicon quaternary ammonium salt, which belongs to the technical field of textile chemistry. The method of the invention is to strengthen the adhesion density of the organosilicon quaternary ammonium salt to the cotton fiber and improve its antibacterial performance after finishing. The cotton yarn is impregnated with neutral glutamic acid solution, compounded organic silicon quaternary ammonium salt, and weak acid rinsing solution in sequence, and finally baked to complete the finishing, that is, the fiber is negatively charged by pretreatment with neutral 5% glutamic acid to improve For the electrical adhesion of positively charged organosilicon quaternary ammonium salts, use 2% compound quaternary ammonium salts to make it densely attached, then rinse with weak acid to remove glutamic acid, and bake and coke to attach glutamic acid to remove negative charges. After finishing, the adhesion speed, adhesion density and adhesion efficiency of cotton fiber to organic silicon antibacterial quaternary ammonium salt are improved, the antibacterial performance of cotton fabric after finishing is enhanced, and the appearance properties such as softness and moisture retention of finished cotton fabric are improved at the same time. The process is simple, the operation is convenient, the consumption is low and the efficiency is high, and it has application value for finishing cotton yarn for filtering bacteria, preventing bacteria, killing bacteria and killing viruses.