The invention discloses a heat-resistant flame-retardant polyester, a polyester product, and a preparation method and application thereof. The preparation method of the heat-resistant flame-retardantpolyester comprises the following steps: carrying out copolymerization reaction on a first mixed reaction system containing a phosphorus-containing compound, binary acid and / or binary acid ester, dihydric alcohol and an esterification and / or transesterification catalyst to obtain an intermediate product; and continuously reacting a second mixed reaction system containing the intermediate product,a polycondensation catalyst and a stabilizer under a vacuum condition to obtain the heat-resistant flame-retardant polyester. The phosphorus-containing compound has a structure as shown in the following formula, according to the invention, a phosphorus-containing compound is introduced into a synthesis system; the 2, 5-furandicarboxylic acid-based polyester has the advantages that the glass transition temperature and flame retardant property of the 2, 5-furandicarboxylic acid-based polyester can be effectively improved, so that the formed copolyester has excellent heat resistance and flame retardance, and can be widely applied to the fields of fire-fighting products, kitchen electrical products, food packaging, optics, building materials, decorative materials, automobile manufacturing, barrier films, barrier bottles, fibers, engineering plastics and the like.