With the trend of reduction in depth of focus, the control of wafer surface is becoming more and more important. The control of wafer surface in dual-stage lithography is studied. The focus detection method, which is based on the polarization modulation mechanism of dual-grating moiré fringes and its measurement principle, is introduced; then the focusing and leveling technique in dual-stage lithographic system is studied. The algorithm for defocus in exposure slit is evolved by using least square method, surface fitting with a plane and coordinate translation. The defocus-decoupling algorithm is studied in detail, which converts the defocus to movement of the piezoelectric ceramics (PZT) and prevents the shift for the center of the exposure slit. The algorithm can be used for precision of 10 nm in focusing and leveling by the simulation, which can meet the need of projection step scan lithography machine with line width less than 100 nm.