Conflicts in transmigration areas are generally multidimensional and influenced by social, economic, land, and institutional factors. This study aims to identify the forms and distribution of conflicts in three districts of the transmigration area, namely Momi Waren District, Ransiki District, and Oransbari District, as well as to formulate a smart system-based conflict resolution approach through the use of spatial data, local institutions, and local wisdom-based settlement practices. Based on field mapping, four main categories of conflict were identified: 1) Land conflicts occur throughout the transmigration sites in the form of claims to transmigration land that has not been handed over to transmigrants because the compensation price is below normal. In addition, there is no ATR BPN office in South Manokwari Regency, one of whose functions is community empowerment and conflict resolution. 2) Economic conflicts occur because transmigrants are registered and recorded in the population registry, making it easy for them to access capital. Several economic activities in agriculture and transportation services are dominated by transmigrants, causing economic jealousy. 3) Social conflicts occur when the distribution of social assistance is uneven and the excessive use of illegally sold alcoholic beverages causes social unrest. 4) Institutional conflicts occur when civil servants, police, and military personnel are recruited, and not all indigenous Papuans who are nominated can be accommodated, requiring the involvement of tribal councils to formulate recommendations for recruitment that prioritize indigenous Papuans. The root causes of the conflict were analyzed using a root cause analysis approach that covered unclear land boundaries, unequal economic access, weak coordination between institutions, and low social trust due to differences in interests between groups. This study utilizes best practices from the Tribal Council, the South Manokwari Regency Transmigration and Manpower Office, the Religious Harmony Forum, and the Social Services Office as the basis for developing smart maps for an early warning system for conflicts. The results of the study formulate a Smart Conflict Resolution System framework consisting of three main components: (1) participatory spatial mapping of conflicts and key actors, (2) integration of institutional databases and social-customary mediation channels, and (3) design of smart maps as a mitigation and decision-making tool in transmigration areas. This system is expected to strengthen collaborative governance, prevent conflict escalation, and realize inclusive and sustainable management of transmigration areas