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Ultra-precision measurement systems are important for semiconductor manufacturing processes. In a phase grating sensing alignment (PGA) system, the measurement accuracy largely depends on the intensity of the diffraction signal and its signal-to-noise ratio (SNR), both of which are associated with the grating structure. Although an equally segmented grating structure could increase the signal of a high odd order, it could also strengthen the signals at the zeroth and even orders which are the main contributors of stray light. This paper focuses on the practical problem of differently responding diffraction orders but in one grating structure. An analytical relationship has been established between the diffraction efficiency and the segment structure of phase grating. According to this analytic model, we then propose a design method to increase the diffraction signal at high odd orders and, meanwhile, to decrease it at the zeroth and even orders. The proposed method provides a fast and effective way to obtain the globally optimal grating structure in the valid scope. Furthermore, the design examples are also verified by means of numerical simulation tool–rigorous coupled-wave analysis (RCWA) software. As a result, the proposed method gives insight into the diffraction theory of segmented grating and the practical value to greatly improve the design efficiency.