Stunting remains a major public health challenge in Indonesia, characterized by significant regional disparities and complex multidimensional determinants. Effective intervention strategies therefore require analytical approaches that are capable of capturing spatial heterogeneity and identifying region-specific vulnerability patterns. This study applies Fuzzy Geographically Weighted Clustering (FGWC) optimized using the Flower Pollination Algorithm (FPA) to map district-level stunting vulnerability and identify priority intervention areas. The analysis covers 514 districts using 21 multidimensional indicators representing health, nutrition, housing conditions, food security, social protection, and demographic characteristics derived from the Central Statistics Agency. The integration of FGWC with FPA enhances clustering performance by incorporating spatial dependence and metaheuristic optimization, enabling the algorithm to produce more stable and geographically sensitive clusters. Cluster validity indices confirm that a four-cluster solution provides the most optimal segmentation of stunting vulnerability. The results reveal distinct regional structures, socioeconomic-driven vulnerability associated with limited asset ownership, high dependence on social assistance and large household size, multidimensional deprivation concentrated primarily in eastern Indonesia, and nutrition-related vulnerability linked to breastfeeding duration and food security. These findings demonstrate that stunting patterns in Indonesia are spatially heterogeneous and influenced by diverse structural factors. The proposed FGWC–FPA framework offers a robust geospatial optimization approach that can support more precise, evidence-based, and region-specific strategies for accelerating stunting reduction.