Through the petrographic studies, it is found that the carbonate rocks in Northern Tarim Basin have developed a diagenetic paragenetic sequence of silicification → hydrothermal dolomitization → calcitization. It is also found that the hydrothermal diagenetic fluids have been mixed with organic carbon, meteoric water or the 87Sr rich formation water in different degree. The carbonate rocks in the research area have a corresponding diagenetic response to the “magmatic hydrothermal fluids-formation water compound fluid system”. The magmatic hydrothermal fluids is an important source of Si and REE to the diagenetic fluid flow and is also a heat source that drives the magmatic hydrothermal fluids and formation water cycle underground.