The intercalation of magnetic atoms into van der Waals (vdW) gaps offers a versatile approach for manipulating local magnetic ordering in vdW magnets. However, these intercalated magnetic atoms are often intricately positioned within the gaps, resulting in an ambiguous impact on local magnetic interactions and spin configurations. Herein, the atomic and magnetic structures of self‐intercalated prototype materials Cr1+δTe2 are comprehensively investigated using transmission electron microscopy, elucidating the correlation between the concentration and distribution of intercalated Cr atoms and the evolution of spin textures. The observed transitions from topological Néel‐type skyrmions to non‐topological type‐II bubbles, and ultimately to trivial ferromagnetic domains, underscore the complex nature of these magnetic spin textures. The complexity of the local structural arrangements is further revealed through integrating atomic‐resolution imaging, revealing the disorder‐order‐disorder transitions manifested by the distribution of intercalated atoms. The modulation of intercalated atomic structure shapes the observed spin textures by affecting the Dzyaloshinskii−Moriya interaction (DMI), inter/intra‐layer coupling, and magnetic anisotropy. These findings provide profound insights into the structure‐magnetism relationship, offering promising avenues for engineering the magnetic properties of vdW magnets at the atomic level.