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Color centers in 2-dimensional hexagonal boron nitride (h-BN) have recently emerged as stable and bright single-photon emitters (SPEs) operating at room temperature. In this study, we combine theory and experiment to show that vacancy-based SPEs selectively form at nano-scale wrinkles in h-BN with its optical dipole preferentially aligned to the wrinkle direction. By using density functional theory calculations, we find that the wrinkle curvature plays a crucial role in localizing vacancy-based SPE candidates and aligning the defects symmetry plane to the wrinkle direction. By performing optical measurements on SPEs created in h-BN single-crystal flakes, we experimentally confirm the wrinkle-induced generation of SPEs and their polarization alignment to the wrinkle direction. Our results not only provide a new route to controlling the atomic position and the optical property of the SPEs but also revealed the possible crystallographic origin of the SPEs in h-BN, greatly enhancing their potential for use in solid-state quantum photonics and quantum information processing.