The heat transfer mechanism during laminar cooling before the down coiler of the run-out-table (ROT) process is a metallurgical key for maintaining the quality of the steel strip. Large variation of the temperature profile along the strip forms residual stress, resulting in the strip distortion. This study developed a computational model through the commercial software Simufact (TM) to analyze the temperature history and deformation, for the purpose of precisely predicting the behaviors of phase transformation during laminar cooling on ROT. This model simulated a specific case, HM690T, provided by the steel factory of which the mechanical properties are computed through JMatPro (TM). The model was first verified in accordance with the field data of temperature profile and experimental measurements of residual stress obtained from the steel company, based on the cooling process provided by the top and bottom water banks. The simulation model was then applied to predict the deformations at each cooling stage and the secondary deformations resulted from alternative cooling of water and air. In addition, the stresses, deformation, and phase transformation for various cooling patterns and cooling periods were simulated based on the developed model, and the optimal ratio of cooling periods of the top and bottom banks was determined. The analysis helps solve the problem of strip flatness during cooling stage on ROT.