Scanning beam interference lithography (SBIL) is an advanced technology developed for manufacturing large-area diffraction grating at a nanometer-scale phase accuracy. To withstand environmental disturbances and maintain the interference fringes still relative to the substrate, SBIL requires high-precision phase control. We proposed a fringe phase control system with homodyne detection for SBIL. First, a homodyne detector is employed to achieve high-precision phase measurement, while ensuring the simplicity of the optics and high laser utilization. The time-varying nonlinear error in the measurement results is corrected by a dynamic ellipse fitting method. To reduce the latency effect, a lead controller is designed using the root locus method based on the model identification result. The lead controller considerably increases the control bandwidth while ensuring a sufficient phase margin, which further suppresses disturbances and stabilizes the interference fringes to within ∼1  /  60 of the fringe period. Wide-range phase tracking for perpendicular scanning with high accuracy is also verified through an experiment.