Hydrate phase transition may bring hidden dangers for well control safety, even accidents of blowout happen in deep water drilling. Accurate calculation of all the drilling parameters is of great importance for well control safety. In this study, the mathematic models of transient heat transfer and multiphase flow have been established with the consideration of hydrate phase transition. Furthermore, the position where hydrate formation is most likely to occur was predicted with the proposed models, and the factors affecting hydrate formation region were also analyzed. Finally, the analysis of the effect of gas hydrate phase transition on some important parameters in well control, such as the pit gain, gas void fraction, and bottom hole pressure, is presented. The results show that hydrates form near the mud line during the drilling and shut‐in stage, but the hydrate formation region will be narrowed as well killing start. Additionally, the hydrate formation region decreased with the increase of flow rate and increased with the increasing shut‐in time, hydrate inhibitors, and riser insulation are presented to prevent hydrate blockage. More importantly, the gas void fraction and pit gain decrease due to the formation of hydrates, leading to the gas kick early detection not timely and gas kick more “hidden.”