To improve the flame retardant efficiency of aromatic Schiff base (BA), and adjust the crosslinking temperature of imine groups, a cyano group, an electron-drawing group has been introduced into the chemical structure of aromatic Schiff base to obtain a third monomer for poly(ethylene terephthalate) (PET), named as dimethyl-5-[(2-cyanobenzylidene) amino]-isophthalate (CBAA). Thermogravimetry-differential scanning calorimetry (TG-DSC) and dynamic rheological results prove that the PET-based copolyester containing CBAA (CBAAnPETs) can crosslink at higher temperature than that containing BA, which will not affect the preparing and processing of PET. DSC and wide angle x-ray diffraction (WAXD) results demonstrate CBAAnPETs remain good crystallization ability. Owing to the two types of cross-linking reactions, i.e. the reactions between Schiff base (-CH=N-) and cyano group (-C= N), and among -CH=N-units, CBAA plays an important role in solid phase as well as gaseous phase endowing CBAAnPETs with excellent flame retardancy. With a low CBAA content (only 6.7 mol%), the copolyesters self-extinguish in 5s with no melt drips in UL-94 vertical test, and its LOI value also increases to 31.0%. The peak heat release rate and total smoke release of the copolyesters obtained from cone calorimetry also observably decrease.