Defect-induced magnetism in two-dimensional (2D) materials holds enormous potential for next-generation spintronic and quantum devices, yet its realization beyond monolayer remains elusive. In this work, we investigate the emergence and modulation of magnetism in multilayer PtSe₂ via a combined theoretical–experimental approach, integrating hybrid density functional theory (DFT) calculations with aberration-corrected scanning transmission electron microscopy (AC-STEM). In multilayer PtSe₂ with the presence of Pt vacancies, magnetism is typically quenched due to interlayer interactions, but it can be restored by complex defect structures comprising, in addition to a Pt vacancy, a Pt_Se antisite. These configurations induce magnetic moments of up to 3.16 µ_B and give rise to a two-dimensional half-metallic state in bilayer PtSe₂, which is highly desirable for spin-polarized transport. Furthermore, the electronic and magnetic properties can be tuned by nearby Se vacancies, which drive transitions between different types of magnetic states. When embedded in the middle layer of trilayer PtSe₂, this combination of defects extends the magnetic moments beyond the defect-carrying layer. Overall, these findings demonstrate that defect engineering enables robust magnetic phase control and spin-filtering behavior without external doping or strain, establishing PtSe₂ as a tunable 2D magnetic material platform for scalable, room-temperature spintronic and valleytronic applications.