Agrochemical use, GHG emissions, and gross domestic product (GDP) vary widely across Southeast Asia, making the region suitable for cluster-based sustainability analysis. This study applies hierarchical clustering analysis (HCA) to classify nine Southeast Asian countries using four standardized indicators: pesticide use, nitrogen fertilizer use, GHG emissions, and GDP. Exploratory data analysis reveals significant disparities, with Brunei and Indonesia emerging as outliers due to exceptionally high input intensity and emissions, respectively. HCA identifies four distinct clusters: (1) low-input, low-emission economies (Cambodia, Laos, Myanmar); (2) moderately intensive systems (Malaysia, Thailand, the Philippines, Vietnam); (3) a high-pesticide profile (Brunei); and (4) a high-emission, high-output outlier (Indonesia). Principal Component Analysis confirms the cluster structure and highlights variation in emission efficiency. The findings show that similar agroecological contexts can yield divergent environmental outcomes, emphasizing the role of policy and technology. This study provides the first region-wide, data-driven typology of agricultural sustainability in Southeast Asia using HCA.