The invention discloses a flame-retardant antibacterial polyester-cotton blended fabric and a manufacturing method thereof and belongs to the technical field of functional textiles. The technical scheme adopted by the invention comprises the key points of: adopting a rolling-baking process to carry out multifunctional finishing on the polyester-cotton blended fabric, firstly dissolving a flame-retardant agent (CP), an antibacterial agent (chitosan), a crosslinking agent (citric acid), sodium hypophosphite, a penetrating agent (JFC), a protective agent (non-ionic emulsion fiber of water-solubleoxidized polyethlene wax) and phosphoric acid in water to prepare finishing liquid, then feeding the polyester-cotton blended fabric into the finishing liquid to dip for 5-20 minutes, and then carrying out twice dipping and twice rolling, wherein the pick-up rate after rolling is 70%-100%; drying the polyester-cotton blended textile at a temperature of 60-90 DEG C, baking at a temperature of 130-160 DEG C, and then drying after washing to obtain the flame-retardant antibacterial polyester-cotton blended fabric. The flame-retardant antibacterial polyester-cotton blended fabric and the manufacturing method disclosed by the invention have the beneficial effects that by adoption of the finishing system, the process flow is shortened, the operation is simple, and the standards of ecological textiles and the requirements of environmental protection as well as the needs of sustainable development are met.