Afaq Khoja (1626–1694) was a significant figure in the spiritual and political history of Uyghur society whose authority emerged at the intersection of Sufi legitimacy and political power in Xinjiang. This study examines how Afaq Khoja developed a spiritual-political network through the Naqshbandi Order and how it contributed to Uyghur collective identity during 1671–1694. Employing a socio-intellectual historical method and a socio-historical approach, the study analyzes the institutional networks, circulation of religious knowledge, and Sufi practices surrounding his leadership. The findings show that Afaq Khoja transformed Naqshbandi networks into an integrated system of spiritual authority, social organization, and political mediation. His religious legitimacy, reinforced by karāmah narratives and charismatic leadership, facilitated the expansion of the order across diverse social groups. Ritual practices, knowledge transmission, institutional structures, and collective narratives strengthened communal cohesion and shared religious-cultural consciousness. The study argues that Afaq Khoja’s significance lay in institutionalizing spiritual networks as mechanisms of social cohesion and collective identification, demonstrating how Sufi institutions could simultaneously function as religious, social, and political structures in seventeenth-century Central Asia.