To explore the effect and mechanism of bivalent ion doping on yttrium iron garnet (YIG), Zn-YIG (Zn-doped YIG) nanoparticles with a size of 60~70 nm were prepared by the sol-gel method. It was proven that Zn ion doping resulted in lattice expansion and internal stress due to crystallite size shrinkage. A Raman spectroscopic analysis proved the influence of Zn doping on the crystal structure and peak intensity by analyzing Raman vibration modes. The characteristics and chemical mechanism of mass loss and phase evolution in each temperature region were explored through TG-DSC measurements. Moreover, it was revealed that the antiferromagnetic coupling, pinning mechanisms and particle aggregation lead to coercivity, exhibiting different variation trends. A saturation magnetization (Ms) curve variation mechanism was further revealed, which was due to the thermal effects, super-exchange effect, and coupling effect between sub-lattices. Meanwhile, the influence of the thermal effect on Ms and its mechanism were explored by spin theory, and it was proven that it was mainly caused by the random arrangement of magnetic moments and thermal vibration. These results provide theoretical support for the wider application of YIG devices in microwave and high-temperature fields.