The structural evolution of polyacrylonitrile fibers in stepwise heat treatment process and its relationship with properties were investigated systematically.Results demonstrated that the cyclization degree and dehydrogenation index of fibers reached 84.13% and 1.361, respectively after stabilization at 265 C.The oxygen reaction was enhanced after stabilized at 245 C. Refinement of the microcrystalline structure took effect during stabilization and low temperature carbonization, while growth of microcrystalline dominated during high temperature carbonization. The results of surface topography study not only provided the evolution characteristics of surface microstructure under the influence of chemical reaction, but also further complements the internal aggregation structural rearrangement process from the side. Additionally, the temperature zone from 245 to 265 C was the key stage of the formation of the skin-core structure, which would be transmitted to the resultant carbon fiber.Tensile strength and tensile modulus decreased during stabilization stage, reaching 4.273 GPa and 221.132 GPa, respectively after high temperature carbonization. The elongation at break which first increased and then decreased proved a toughness failure to brittleness failure. The investigation elucidated the relationship between the mechanical property with chemical and physical microstructure. And the possible rearrangement process of the aggregation structure was proposed.