The invention relates to an antibacterial finishing method of cotton fabrics. The finishing method comprises the following steps: preparing a nano zinc oxide complex solution, preparing a quaternary ammonium salt polymer solution; mixing the nano zinc oxide complex solution and the quaternary ammonium salt polymer solution to obtain a zinc oxide-quaternary ammonium salt polymer composite antibacterial agent; mixing the zinc oxide-quaternary ammonium salt polymer composite antibacterial agent with water to obtain an antibacterial finishing solution with a concentration of 50 to 500 g/L; using the antibacterial finishing solution to carry out a dip padding treatment on cotton fabrics, and finally drying the cotton fabrics after the dip padding treatment. The adopted antibacterial finishing agent is a complex of quaternary ammonium salt polymer and nano zinc oxide. The cotton fabrics processed by the provided antibacterial finishing method have a good antibacterial performance. The using amounts of two antibacterial agents can be flexibly adjusted according to the actual needs; the local antibacterial effect is enhanced, at the same time, the binding strength between the antibacterial finishing agent and cotton fabrics is strong, the cotton fabrics are resistant to washing, and the antibacterial effect is long-lasting.