The invention relates to a multiple dispersed phase flame retardant shear thickening fluid, its preparation method and an application thereof, and belongs to the technical field of nano materials. The preparation method of the multiple dispersed phase flame retardant shear thickening fluid comprises the following steps of: firstly, respectively fusing 100 parts by weight of a disperse medium at the temperature of 30-60 DEG C, adding 40-70 parts by weight of hard spherical nanoparticles, dispersing at the temperature of 30-60 DEG C for 40-70 minutes, adding 1-10 parts by weight of a carbon material and simultaneously adding 10-20 parts by weight of a disperse medium, and continuously dispersing at normal pressure for 1-4 hours, so as to obtain a multiple dispersed phase fluid with a substantial shear thickening characteristic. The viscosity is 100-100000 Pa.S / 25 DEG C and the flame retardancy reaches UL-94V-0 level. By reasonable design and application of the nanometer effect of the hard spherical nanoparticles and characteristics of the carbon material, the multiple dispersed phase flame retardant fluid with the substantial shear thickening characteristic is prepared. Through an ultrasonic technology, a spraying technology, a sizing technology, loading and thermal sewing technologies, the multiple dispersed phase flame retardant shear thickening fluid can be used for impregnation composition, coating composition or embedding composition of fabrics, so as to prepare a light-duty flexible soft protection material with a flame retardant function.