The invention discloses a flame retardant acrylonitrile butadiene styrene (ABS) composition with high heat resistance and high toughness and a preparation method and the application of the composition; the flame retardant ABS composition comprises the components in parts by weight: 100 parts of high temperature resistant ABS masterbatches, 10-25 parts of environment-friendly brominated flame retardant, 5-10 parts of flame retardant synergist, 0.5-2 parts of maleic anhydride grafting styrene block copolymer (SEBS), 5-15 parts of flexibilizer and 0.5-5 parts of processing agent. The preparation method of the flame retardant ABS composition comprises two steps of: firstly, preparing the high temperature resistant ABS masterbatches; and secondly, mixing the temperature resistant ABS masterbatches, the environment-friendly brominated flame retardant, the flame retardant synergist, the maleic anhydride grafting SEBS, the flexibilizer and the processing agent, adding the mixture into a twin-screw extruder and then carrying out extruding and pelleting to obtain the flame retardant ABS plastic particles with high heat resistance and high toughness. The flame retardant ABS composition with high heat resistance and high toughness has high heat resistance, impact resistance and flame retardant effect as well as excellent stability and mechanical property, thus being widely applied to the fields such as a motor, a blower, a power supply box, a microwave oven, an electric cooker, an extension socket, an automobile instrument, a heat-resistant storage battery and the like.