As the important means of “drilling down into deep earth”, scientific deep drilling and ultra-deep drilling become important methods, which are known as “telescope into the earth’s crust”. Ultra-high temperature and high pressure in scientific ultra-deep well is one of the most prominent technical difficulties in drilling operation, so rigorous standards were put forward to the drilling fluid, down-hole motor, aluminum alloy drill pipe and so on, the project becomes more difficult with higher risk and prolonged construction duration. This paper summarizes the characteristics of scientific ultra-deep drilling engineering and analyzes the effect of drilling fluid continuous circulation on borehole stability and downhole temperature, it is concluded that scientific ultra-deep well has strong technical demand for continuous circulation system and this system would provide technical support for future scientific ultra-deep drilling program in China.