Lithography motion stages widely adopt a coarse-fine compound architecture to achieve both large strokes and nanometer-level precision. However, during high-speed scanning, coarse-fine parasitic coupling—induced by flexible cables and voice coil motor eddy currents—severely limits the fine stage''s positioning performance. To address this, we propose a decoupling compensation algorithm combining gray-box physical modeling and a state-space disturbance observer (SS-DOB). The complex coupling disturbance is explicitly decomposed into deterministic stiffness and damping components, alongside a nonlinear residual. By identifying the stiffness online via constant-velocity excitation and the damping through frequency-domain analysis, zero-phase-lag feedforward compensation is achieved for the dominant coupling forces. Simultaneously, an SS-DOB with digital timing compensation accurately estimates and suppresses high-frequency residuals. Experimental results on a lithography motion stage validate the method, demonstrating a 43% improvement in Y-direction positioning accuracy (Mean+3σ) from 32.73 nm to 18.67 nm.