Micromorphology is further studied on the basis of our previous researches concerned with the nano-micron FeS2 whisker. There are obvious differences in the intensive degree, diameter and micromorphology among the FeS2 whiskers growing in different stages. From the early to late stage, the intensive degree increases, the diameter decreases, and the surface micro-morphology changes following the regularity: protrusive nodulation → coarse → smooth → flat. According to the theory of crystal growth, the geological setting and processes of whisker formation, we discuss the stability and evolution of crystal growth interface of FeS2 whisker occurring in Gengzhuang gold deposit (Shanxi Province, China). The results suggest that the negative temperature gradient and the supercooling appear in the early stage of the whisker growth, whereas the positive temperature gradient of reposeful state appears in the late stage. In the whisker growth stage, the component concentration changes through the three stages: severely nonhomogeneous in the early stage, relatively homogeneous in the middle stage, more homogeneous in the late stage. The general changing process of the interfacial state is from unstable to stable. Micromorphology of FeS2 whisker in Gengzhuang is the result of synergism of temperature, component concentration and stability of crystal interface phase in hydrothermal system. The micromorphology not only reflects the physical and chemical characteristics of the hydrothermal system during the whisker growth, but also indicates the stability characteristics of the interface phase and records the changing process of the whisker growth.