The traditional megalithic villages in Sumba and Ngada hold cultural tourism potential and strong emotional ties to the indigenous community. Rapid sociocultural development and shifts in ideology and technology have caused several traditional megalithic villages to lose their “originality.” This study examined the traditional villages’ sustainability status from five dimensions: socio, culture, environment, economics, and technology and infrastructure. A comparative study has been performed on the traditional villages’ management system to explore the role of the indigenous community and local wisdom and the underlying factors. This research applied mixed methods with a comparative descriptive approach based on Multidimensional Scaling (MDS) analysis results. MDS analysis results indicated that several traditional villages in Central Sumba have weak sustainability with socio-culture as the leverage factor. Conversely, traditional villages in Ngada Regency exhibited different results as they have strong sustainability status with socio-culture as the main leverage factor. This is due to the factors of the status of institutions that manage the traditional village, the indigenous community’s resistance and adaptation, local wisdom, support from external parties, and the improvement of cultural attraction. The indigenous community’s understanding of their role as the owner, actor, and preserver of their culture is the key to cultural tourism sustainability.