Cr1+δTe2, a two-dimensional van der Waals ferromagnet, displays a contested magnetic structure, poised between collinear and non-collinear spin configurations. In this work, we elucidate the microscopic magnetic structure of Cr1.33Te2 by combining single-crystal neutron diffraction, X-ray absorption spectroscopy, angle-dependent magnetocrystalline anisotropy study, and first-principles calculations. Neutron diffraction measurements reveal a distinct collinear spin alignment, whereas spectroscopic analyses reveal inherent structural vacancies at both Cr and Te sites. These vacancies lead to local symmetry breaking that lifts the orbital degeneracy of the Cr 3d states, as demonstrated by our first-principles analysis. The resulting modification of magnetocrystalline anisotropy emerges as the key mechanism stabilising the collinear magnetic ground state over the non-collinear one in the presence of vacancies. Our findings uncover a vacancy-driven route to control spin anisotropy and magnetic ordering in layered van der Waals magnets, providing a microscopic framework for the design of tunable 2D magnetic materials.