Phase stability of GaN on (111)–(001) nanoscale faceted Si is investigated. Nanoscale faceting (nanofaceting) is accomplished on a Si(001) substrate with interferometric lithography and anisotropic wet etching. By relying on the nucleation and associated lateral growth depending on orientation and crystal structure, spatial separation of a cubic-phase region from hexagonal-phase GaN regions which initiate on the facing Si(111) sidewalls of a 355-nm period V-grooved Si surface is achieved. The appearance of cubic-phase region is associated with a rapid surface planarization with its principal crystal axes parallel to those of the Si(001) substrate. The boundary between cubic and hexagonal phases is revealed along the Si(111) sidewalls and extends from each V-groove to the GaN surface for a 600-nm deposition. The phase separation of GaN selectively grown on a nanoscale faceted Si surface and the comparison of its material properties (photoluminescence and Raman scattering for stress measurement) with those of GaN grown on wide-area Si(111) and Si(001) imply that nanofaceting can be utilized for phase control of GaN on a Si(001) substrate.