Modern wireless communication and radar systems urgently require the application of low-loss and high-permittivity yttrium iron garnet (YIG) ferrite for highly efficient and integrated microwave circulators, isolators, filters, etc. However, achieving a high dielectric constant, low dielectric loss, and narrow ferromagnetic resonance (FMR) linewidth simultaneously is challenging. Here, we synthesized Bi–Ca–Zr co-substituted YIG ferrites and comprehensively investigated the effects of multi-ion substitution on the polycrystalline microstructure and microwave electromagnetic properties of the material. The introduction of Bi³⁺ ions at the crystallographic dodecahedral sites enhances the electronic polarization of single Fe³⁺ ions and the superexchange interaction between them. The substitution ofZr⁴⁺ ions for Fe³⁺ ions at octahedral sites suppresses the FMR linewidth broadening caused by magnetocrystalline anisotropy. Moreover, multi-ion substitution results in competition between liquid phase sintering and grain boundary pinning and influences the densification and grain growth processes, resulting in a non-uniform and dense microstructure composed of crystallites with a bimodal size distribution. This distinctive morphology further contributes to FMR linewidth reduction and permittivity increase. The optimized Bi–Ca–Zr co-substituted YIG ferrite has a narrow FMR linewidth of 33 Oe, high permittivity of 27, and high Curie temperature of 200 °C, making it a promising candidate for next-generation microwave devices.