In order to explore the effect of segregation on the long-term water stability of asphalt mixture in hot and humid area, two simulation schemes of gradation segregation and temperature segregation were designed respectively. The void ratio of the asphalt mixture was tested by the drainage method, and the residual stability of the asphalt mixture was tested by the immersion Marshall test. Based on the nonlinear fitting method, the datas of residual stability of the asphalt mixture with different dry-wet cycles were analyzed, and the decay curves and the law of water stability of asphalt mixture were obtained under different states of segregation. The research results show that with the dry-wet cycles progress, the void ratio of asphalt mixtures with different types of segregation increases, but the increase is limited. After ten times of dry-wet cycles, the residual stability is 81.8%, indicating that the fine aggregate segregation is not easy to cause strength loss under the dry-wet cycles. Under the condition of severe segregation, the residual stability decreases to 79.8% after the first dry-wet cycle, and then decreases to 67.4% after the 10th dry-wet cycles. Whether there is segregation or not, the effect of dry-wet cycles has a turning point, that is, the effect of dry-wet cycles in the early stage is obvious, and the effect significantly slows down after reaching the turning point. As the degree of segregation increases, the turning point of the residual stability gradually moves forward, indicating its long-term water stability becomes worse.