A phosphorus containing polysiloxane flame retardant and antibacterial agent has been synthesized and applied to cotton fabrics. A treatment method has been implemented to achieve the dual function of flame retardant and antibacterial on cotton fabrics, Achieve two things at one stroke. This flame retardant method can effectively avoid the problem of formaldehyde release from fabrics treated with phosphorus containing flame retardants. Amino silicone oil and p-bromobenzaldehyde are used to synthesize intermediate products, phosphite, 5,5-dimethylhydantoin, and phosphite to obtain halogenated amine precursors (DPTMS). The VFT and LOI results indicate that this additive can effectively improve the flame retardancy of fabrics. Thermogravimetric analysis shows that the residual carbon content of DPTMS/Cotton can reach 9.1% and 24.7% under air and nitrogen conditions, respectively, indicating that DPTMS can effectively improve the thermal stability of cotton fabrics. The cone calorimetry test showed that the total heat release of DPTMS/Cotton was significantly reduced by 49.8% compared to that of Cotton. After being heated, polysiloxane provides a more solid carbon layer, which has a suffocating effect on the flame. The results of antibacterial test are surprising, and the antibacterial rate of DPTMS/Cotton against E. coli and S. aureus can reach more than 99%.