Phosphorus/nitrogen flame retardant ammonium three phosphoric acid glycerol ester (FR) with reactive -P-O−NH4+ groups was synthesized from glycerol, phosphoric acid and urea. At high temperature, the -P-O−NH4+ group in FR is decomposed into -P-O−H+ group. Under the action of catalyst dicyandiamide, -P-O−H+ forms phosphonic anhydride. Phosphonic anhydride can dehydrate and condense with the hydroxyl group on the 6-position carbon atom in the glucose ring of cotton fiber, forming a firm P-O-C bond, thus fixing FR molecule firmlyon cotton fiber. XRD suggested that the finishing process only slightly affected the cotton fiber structure and the surface morphology, elemental composition of char residues in cotton fabrics were tested by scanning electron microscope (SEM) and energy dispersive spectrometer (EDS). Confirmed that FR was grafted well with slight damage to the cotton structure. When the treated cotton with 25.3% weight gain(WG) in FR, the treated cotton has self extinguishing property and passed UL-94 vertical burning V-0 classification, the limiting oxygen index (LOI) was improved from 17.0–40.5%, and the LOI can still reach 30.9% after 50 laundering cycles, the cone calorimetry(CONE) analysis indicated that the peak heat release rate (PHRR) of the treated cotton was reduced from 190.3 kW/m2 to 17.9 kW/m2, and the total heat release (THR) was reduced from 2.8 MJ/m2 to 1.8 MJ/m2, The thermogravimetric(TG) and Differential scanning calorimeter (DSC) showed that the addition of FR inhibited the initial thermal degradation temperature of the treated cotton under heating conditions, and TG showed that the initial thermal degradation temperature of treated cotton in nitrogen and air was 225.9 ℃ and 221.8 ℃, respectively, which was lower than that of untreated cotton. The mechanical properties are in the usable range, which showed that treated cotton have excellent flame retardancy, durability and good flexibility.