Agent-based simulation is a useful approach for the analysis of dynamic population evolution. In this field, the existing models mostly treat the migration behavior as a result of utility maximization, which partially ignores the endogenous mechanisms of human decision making. To simulate such a process, this article proposes a new cognitive architecture called the two-layered integrated decision cycle (TiDEC) which characterizes the individual’s decision-making process. Different from the previous ones, the new hybrid architecture incorporates deep neural networks for its perception and implicit knowledge learning. The proposed model is applied in China and U.S. population evolution. To the best of our knowledge, this is the first time that the cognitive computation is used in such a field. Computational experiments using the actual census data indicate that the cognitive model, compared with the traditional utility maximization methods, cannot only reconstruct the historical demographic features but also achieve better prediction of future evolutionary dynamics.