The invention provides a multilayer-structure-based rare earth permanent magnet and a preparation method thereof. The rare earth permanent magnet comprises a three-layer-structure-based main phase grain and a rare earth-rich phase. The main phase grain has three layers including a nuclear layer, an intermediate layer and a shell layer based on different chemical compositions; and the compositionsinclude R<1>-T-B, R<2>-T-B, and R<3>-T-B correspondingly, wherein the R<1> contains at least one of Ce and La, the R<2> contains at least one of Pr and Nd, the R<3> contains at least one of Dy, Tb, and Ho, the T is at least one of Fe and Co, and the B expresses a boron element. The rare earth-rich phase contains one or more rare earth elements of Ce, La, Pr, Nd, Dy, Tb, Ho, and Gd. According to the invention, a magnet blank is prepared by using the dual alloy process; and then a multilayer-structure-based rare earth permanent magnet is prepared based on a grain boundary diffusion process. According to the rare earth permanent magnet, the formed grain has the three-layer structure and the main rare earth ingredients, in the grain, include light rare earth, medium-and-heavy rare earth, heavyrare earth from inside to outside. The structure is optimized and the coercive force of the magnet is enhanced obviously.