A novel flame-retardant agent, guanidyl- and phosphorus-containing polysiloxane (GPPDMS), was synthesized. The combustion properties of the cotton fabrics treated with GPPDMS were evaluated by cone calorimeter. The results showed that the TTI value of the treated fabric increased and the value of HRR, THR, EHC, and Mass loss decreased. It demonstrated that the treated cotton fabric with GPPDMS generated less combustion heat and obtained better flame retardancy which can be confirmed by the increase of FPI value and the decrease of CO/CO2 ratio. It also revealed that the cotton fabric treated with 18.6 % (add-on) of GPPDMS had highest reduction in heat of combustion. The chemical structures and morphologies of the residues, and the thermal decomposition behavior of cotton fabrics were investigated by FT-IR, scanning electron microscopy, and thermogravimetric analysis, respectively. The results showed that GPPDMS played a protective role on the degradation of cotton fabrics, hindered the formation of volatile species and favored the formation of char. Furthermore, EDS analysis results showed that remarkable amount of Si and P elements were still present on the surface of fibers after combustion; it indicated that the concurrent presence of Si and P in flame retardant effectively enhances the flame retardancy of cotton fabric.