The strips with good flatness after finish rolling will have flatness defects such as edge wave after run-out table cooling. These defects are caused by the residual stress due to inhomogeneous thermal and microstructural behaviors during the cooling stage. The traditional residual stress control methods rely too much on experience, resulting in poor control effect and poor universality. Therefore, this study proposed two residual stress control methods based on model calculation: water flow central crown, and center wave compensation control. The former is mainly based on controlling the uniformity of strip transverse temperature and microstructure. The latter is mainly controlled by mutual compensation of internal stresses. In this paper, the mathematical models of water flow central crown cooling and critical center wave compensation stress were established respectively. Meanwhile, a post-buckling model of hot-rolled strip was established to calculate the aim flatness value at exit of finishing mill under critical compensation stress. Furthermore, a fully coupled finite element model based on temperature, phase transitions, and stress was developed and it was verified using experimental data. Finally, the above two residual stress control methods were realized in the finite element model. The results showed that the two methods can reduce the residual stress and improve the flatness, and the application of center wave compensation control is more effective.