A flame retardant containing two phosphonate structures (DOPO−DP) was synthesized by applying diphenylphosphinic chloride and 10-(2,5-dihydroxyphenyl)-10-hydro-9-oxa-10-phosphazephenanthrene-10-oxide. The DOPO−DP was used to modify the flame retardancy of poly(ethylene 2,5-furandicarboxylate-co-ethylene terephthalate) containing (PEFT). DOPO−DP has a high flame-retardant efficiency in PEFT. The UL-94 V0 level is obtained by adding 7 wt % DOPO−DP into PEFT. The fireretardant mode of action is melting away, which is induced by the plasticizing effect of DOPO−DP mainly. In addition, two chain extenders triglycidyl isocyanurate (TGIC) and 2,2′-(1,3-phenylene)-dioxazoline were applied to enhance the mechanical properties of PEFT. DOPO−DP deteriorates the mechanical properties of PEFT while coupling agents improve the bending and impact strength. While the chain expansion effect of TGIC competes with the plasticizing effect of DOPO−DP, excessive TGIC deteriorates the UL-94 rating of PEFT.