The phase drift leads to low exposure contrast in interference lithography system. In order to effectively suppress the phase drift of interference fringe, an Acousto-Optic Modulator (AOM) was employed to modulate the frequency of interference beam in real time. The characteristic of phase drift was analyzed, indicating that the main disturbance came from air turbulence with frequency within 0~5 Hz. The relationship between phase drift and exposure contrast was deduced by numerical analysis, and the target phase accuracy of fringe locking system was submitted. In terms of the target accuracy, the experiment devices were picked and the experiment system based on RTX was prepared. Finally the parameter model of system was established by closed-loop identification and a feedback controller was designed, thus realizing the fringe locking function. The experiment results indicated that the low-frequency disturbance ranging from 0 to 5 Hz is suppressed efficiently by the proposed fringe locking system under the control frequency of 400 Hz. The 3σ value of phase drift is within ±0.04 period, which satisfies the exposure contrast requirements of interference lithography.