The metamorphism and deformation of rocks can be well recorded by the structures and element distribution of accessory minerals. Especially, the metamorphic/deformation history can be revealed and analysized by in-situ chronologic dating. Apatite is a common accessory mineral in metamorphic rocks. With the rapid development of in-situ dating technology of apatite, it has become an important dating mineral in magmatic rocks and mineral deposit studies. In different metamorphic-deformation processes, a series of important problems about the deformation mechanism and behavior of apatite and its restriction effect on the element diffusion process have not been solved. In this study, rocks in the Eastern Himalayan syntaxis, which has the strongest tectonic deformation and metamorphism, are selected for research. SEM and CL observations show that the apatite in granulite does not show obvious compositional structure, while the apatite in mylonite shows obvious changes in light and dark, that is, composition changes. By statistical analysis of apatite distribution characteristics in thin sections, we found that the long axis direction of apatite in the two metamorphic rocks is approximately parallel to the main foliation. EBSD fabric analysis shows that the apatite in granulite shows obvious intra-granular deformation, while the apatite in mylonite shows almost no intra-granular deformation. The results of EPMA scanning of apatite composition show that the distribution of major elements of apatite in granulite is relatively uniform, while the distribution of Si elements of apatite in mylonite is obviously zonal or uneven, which is consistent with the results of CL scanning. Based on the above apatite deformation and element distribution characteristics, it can be preliminarily concluded that: (1) Although apatite in granulite is directionally distributed parallel to main foliation and occurred intra-granular deformation, it may be due to relative higher metamorphic temperature, which promotes the rapid diffusion of elements and makes the redistribution of elements tend to be uniform. Moreover, the late fluid action occurs element metasomatism along the low-angle grain boundary or near the fracture which are always perpendicular to the maximum tensile stress. (2) The apatite in mylonite is arranged parallel to the mylonite foliation, but almost no intra-granular deformation occurs, possibly due to the low deformation temperature (< 450o), or because the strain of mylonite is mainly concentrated in the quartz and mica domains, while the relatively tough apatite does not participate in deformation. The composition changes shown in the CL image and some major elements distribution maps may be indicating that the low metamorphic/deformation temperature have not led to the rapid diffusion of elements in apatite. (3) The preliminary age results show that the apatite in the granulite records multiple ages, indicating that the inherited apatite occurs in the element redistribution during metamorphism and late stage metasomatize of the apatite which has influence mineral isotope system, while the apatite in the felsic mylonite is the result of continuous fluid activity during the mylonitization process resulting in continuous crystallization of apatite. New results provide important information for the interpretation of apatite age in metamorphic and deformation rocks.