The Mekong Delta is a major rice-producing region in Vietnam and the world, contributing up to 90% of the country’s total rice exports. Here, we report the diversity among mega rice varieties cultivated in the Mekong Delta, focusing on agro-morphological traits, quality traits, and GBSS1 gene variation. Factor Analysis of Mixed Data (FAMD), a multivariate model, was employed to assess quantitative and qualitative traits to determine their relationships. The analysis revealed significant diversity among the varieties, grouping them into six distinct clusters. FAMD analysis provided insights into the interrelationships among traits, identifying key factors contributing to data variance. Grain shape and quality traits emerged as major contributors to the total variance. In addition, the association between disease resistance and leaf color or amylose content was also revealed. These findings suggest that attention should be paid to rice breeding programs. This study underscores the importance of preserving and enhancing the genetic diversity of Mekong Delta rice varieties to ensure continued market competitiveness and adaptability to environmental challenges. The FAMD model is a useful tool for rice breeders aiming to develop breeding programs that combine high yield with desirable quality traits, thus supporting the sustainable development of rice agriculture.