The instability and collapse of the wellbore are the problems that must be dealt with in the drilling engineering. Aiming at the ultra-deep drilling (>6 000 m) process of complex formations, especially discontinuous formations, the stability of the wellbore in complex and special formations is analyzed through the coupling effects of rock mechanical properties, pore seepage, wellbore stress and temperature field. This paper uses the linear superposition principle to combine the thermally induced stress components which caused by the influence of formation seepage, pore pressure changes and changes in the formation temperature field into the in-situ porous elastic model, built up a thermal porous elastic model, and combined the D-P failure criterion and the “stress cloud” idea to establish a wellbore instability analysis model coupled with a porous elastic model and a dynamic temperature field, and the drilling process of an example well in the shallow part of deep water block is validated. The results show that longer drilling circulation time can achieve better formation cooling and hole cleaning effects, but as the circulation time increases, the temperature difference between the wellbore and the formation is too large, and the superimposed thermally induced stress value will increase. The stress difference in all directions of a large rock formation is more prone to instability. The research results broaden the range of application of the previous method of wellbore stability analysis and improve the calculation accuracy.