Abstract3D topological textures have attracted significant attention from researchers due to their distinctive spatial arrangements and intriguing physical properties. However, investigating their topological domain structures at the submicron scale (<1000 nm) proves exceedingly elusive and under‐explored. Here, the size‐dependent behaviors of non‐uniform magnetic domain structures within submicron‐sized FeNi magnetic nanoparticles by micromagnetic simulations are systematically explored. Notably, the existence of magnetic toron‐like structures at the submicron scale and discuss their spatial arrangement and topological properties are identified. Furthermore, critical transition sizes are calculated under various aspect ratios, and the domain structure phase diagram based on nanoparticle size and aspect ratio is constructed. Through visualizations of domain flipping processes and dynamic energy changes, the stable existence of toron‐like magnetic configuration resulting from the competition among demagnetization energy, magnetic anisotropy energy, and magnetic exchange energy are unveiled. Finally, the utilization of core‐shell structures to achieve the stable existence of 3D topological textures are proposed. This work provides important theoretical insights for understanding and designing multi‐domain structures of FeNi nanoparticles at the submicron scale, as well as for constructing topological textures.