During ultra-deepwater shallow drilling, natural gas formed by the shallow gas and decomposing gas of hydrate can easily enter the wellbore to cause the secondary formation of hydrate, and in serious cases, the pipeline is blocked and the drilling safety is affected. In order to simulate the formation of secondary hydrate during drilling in formations containing shallow gas and hydrate, a three-phase flow model is established by considering the hydrate phase transition, solid particle migration and multiphase fluid heat transfer characteristics. The results show that the formation of hydrates in the wellbore largely depends on the injection drilling fluid temperature, displacement and inhibitor concentration. The higher the injection drilling fluid temperature and displacement, the lower the secondary hydrate formation risk. With the addition of thermodynamic inhibitors, the risk of secondary hydrate in wellbore is significantly reduced. When the injection temperature is higher than 20 °C and the displacement is greater than 1800 L/min, there is no secondary hydrate in the wellbore despite the absence of inhibitor. It is an effective way to reduce the risk of secondary hydrate in wellbore by optimizing the injection temperature, displacement and adjusting the inhibitor concentration.