Migration is one of the many responses humans and societies make to ongoing demographic, economic, societal and environmental changes. In this work, we use agent-based modeling (ABM) to study the dynamics of migration flows across provinces and cities in the Mekong Delta, Vietnam. The strength of ABM is that it allows a bottom-up approach that focuses on how individuals make decisions in a complex system comprising various factors. Outputs of our agent-based model are automatically calibrated with actual data using a genetic algorithm. This automated calibration yields some significant improvement in the results, with all observed net- and out-migration data captured within the 95% confidence interval. Sensitivity analysis carried out helps to further understand the impact of critical factors on the final migration decision.