With the increasing demand of higher quality hot rolled strips, flatness defects occurred on the strips during the cooling process on the run-out table have received significant attention and should be considered in the online shape control model. Non-uniform temperature distribution and cooling across the strip width are the main reasons why the strip becomes unflatten after cooling process although the strip is rolled flat at the finishing mill. A thermal, microstructural and mechanical coupling analysis model for predicting flatness change of steel strip during the run-out table cooling process was established using ABAQUS Finite Element Software. In this model, Esaka phase transformation kinetics model was employed to calculate the phase transformation, and coupled with temperature calculation by means of the user subroutine program HETVAL. An elasto-plasticity constitutive model of the material, in which conventional elastic and plastic strains, thermal strain, phase transformation strain and transformation induced plastic strain were taken into account, was derived and realized using the user subroutine program UMAT. The conclusion that the flatness of the steel strip will develop to edge wave defect under the functions of the different thermal and microstructural behaviors across strip width direction during the run-out table cooling procedure was acquired through the analysis results of this model. The calculation results of this analysis model agree with the actual measurements and observation, therefore this model has a high accuracy. To better control the flatness quality of hot rolled steel strip, the shape compensation control strategy of slight center wave rolling is proposed based on the analysis result. This control strategy has been verified by actual measurements, and applied in actual production.