Y chromosome haplogroup O3-M122 is the most prevalent haplogroup in East Asia, and provides an ideal tool for dissecting primary dispersals of the East Asians. Most of the sub-haplogroups of O3-M122 have been sufficiently investigated except for O3a1c-002611, despite its great prevalence and huge population, especially in Han Chinese. In this study, we identified 508 individuals with haplogroup O3a1c-002611 out of 7801 males from 117 East and Southeast Asian populations, typed at two newly discovered downstream Y-SNP markers and ten commonly used Y-STRs. Defined by SNPs IMS-JST002611 (in short, 002611), F11, and F238, three lineages internal to haplogroup O3a1c-002611 have distinct geographical distributions. Furthermore, Y-STR diversity shows a general south-to-north decline, which is consistent with the prehistorically northward migration of the other O3-M122 lineages. The northward migration of haplogroup O3a1c-002611 started about 13 thousand years ago (KYA). The expansions of subclades F11 and F238 in ancient Han Chinese began about 5 and 7 KYA immediately after the separation between the ancestors of the Han Chinese and Tibeto-Burman.