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Abstract The confined defects in 2D van der Waals (vdW)‐layered semiconductors can be easily tailored using charge doping, strain, or an electric field. Nevertheless, gate‐tunable magnetic order via intrinsic defects has been rarely observed to date. Herein, a gate‐tunable magnetic order via resonant Se vacancies in WSe2 is demonstrated. The Se‐vacancy states are probed via photocurrent measurements with gating to convert unoccupied states to partially occupied states associated with photo‐excited carrier recombination. The magneto‐photoresistance hysteresis is modulated by gating, which is consistent with the density functional calculations. The two energy levels associated with Se vacancies split with increasing laser power, owing to the robust Coulomb interaction and strong spin–orbit coupling. The findings offer a new approach for controlling the magnetic properties of defects in optoelectronic and spintronic devices using vdW‐layered semiconductors.