Recent large-scale migration flows from rural areas of the Mekong Delta (MKD) to larger cities in the South-East (SE) region of Vietnam have created the largest migration corridor in the country. This migration trend has further contributed to greater rural–urban disparities and widened the development gap between regions. In this study, our aim is to understand the migration dynamics and determine the most critical factors affecting the behavior of migrants in the MKD region. We present an agent-based model and incorporate the Theory of Planned Behavior to effectively break down migration intention into related components and contributing factors. A genetic algorithm is used for automated calibration and sensitivity analysis of model parameters, in order to validate our agent-based model. We further explore the migration behavior of people in certain demographic groups and delineate migration flows across cities and provinces from the MKD to the SE region.