Freak wave is an extreme sea state with unexpected and huge wave height, which becomes a potential risk for lay barge and offshore pipeline during deepwater installation. In order to investigate the dynamic responses of deepwater S-lay pipeline induced by freak waves, this study developed a comprehensive numerical model with the particular consideration of the freak wave effect. An enhanced superposition method of combined transient wave trains and random wave trains was presented and a series of freak wave trains were generated. The induced pipelay vessel motions were simulated by use of displacement response amplitude operators (RAOs). The pipe-stinger roller interactions in the overbend and the cyclic contacts between the pipeline and seabed soil in the touchdown zone (TDZ) were fully taken into consideration. The developed S-lay model was subsequently utilized to calculate the dynamic responses of pipelay vessel and offshore pipeline under random waves and freak waves for a comparison. The results illustrated the remarkable influence of freak waves on the systematic behaviors of deepwater S-laying pipeline, which offer a significant theoretical basis for pipe structure design and pipelay operation safety.