The high-aspect-ratio silicon grating (HARSG) is an important X-ray optical device that is widely used in X-ray imaging and spectrum detection systems. In this paper, we propose a high-precision alignment method based on the scanning beam interference lithography (SBIL) system to realize precise alignment between the <111> orientation on the (110) wafer plane and the grating lines direction, which is an essential step in HARSG manufacture to obtain the high-aspect-ratio grating structure. After the location of the <111> orientation through fan-shaped mask etching and reference grating fabrication, a two-step method that combines static preliminary alignment and dynamic precision alignment is used to align the reference grating lines direction with the interference field fringes of the SBIL system through the interference of the diffracted light from the reference grating near the normal direction, which can realize a minimal alignment error of 0.001°. Through the overall alignment process, HARSGs with groove densities of 500 gr/mm, 1800 gr/mm, and 3600 gr/mm were fabricated through anisotropic wet etching in KOH solution, producing ultra-high aspect ratios and etch rate ratios greater than 200.