Abstract: In order to ensure the safe exploitation of deepwater natural gas hydrate and reduce the accident risks of the sink of drilling conductor combination system and the instability of hydrate formation, it is necessary to study the setting depth design and vertical bearing capacity of conductor combination system in the three stages of drilling deepwater natural gas hydrate formation, i.e., jetting to the pre-set position and releasing of conductor, cementing of surface casing and urgent separation. According to the theory of pile foundation, the model for calculating the vertical bearing capacity of the drilling conductor under the working conditions in different stages was established to determine the minimum setting depth of the drilling conductor in different operation stages. Afterwards, based on the software TOUGH+HYDRATE and FLAC3D, the model for numerically analyzing the stability of hydrate formation was established to research the stability of hydrate formation in the process of production test. In addition, the safe production test time of hydrate formation was determined according to the Mohr-Coulomb failure criterion. Finally, a case study was carried out on a certain jet drilling operation in the natural gas hydrate formation of the South China Sea. In view of the engineering and geological characteristics of shallow soil and the decomposition of hydrate formation caused by the invasion of drilling fluid, the safe setting depth of conductor is recommended to be 98 m. And in order to ensure the safe bearing load of hydrate formation, it is suggested to set the safe production test time less than 60 d. The research results provide the technical reference for the field operation of drilling conductor in deepwater natural gas hydrate formations.