Interference fringe period is a very important parameter of phase locking in scanning beam interference lithography system (SBIL). According to the feature of the SBIL system, a method that period is measured by moving beam-splitter is proposed. Based on Gaussian beam propagation theory, theoretical error is analyzed. Period counting method is proposed to calculate fringe period. In order to make it easy for two-dimension stage design, measuring period by short-stroke linear stage’s assistance is put forward and experiments are done. The results show that: the method that measuring period by short-stroke linear stage’s assistance is feasible in principle. When fringe density is 1800 line/mm in SBIL system, period measurement repeatability is 1.08 ×10-5 (1σ). Data measured in exposure experiments is consistent with the model, then the feasibility of this method is verified.