The effect of heat treatment on the structure of Poly(p-phenylene benzobisoxazole) (PBO) fiber was studied by wide angle X-ray diffraction (WAXD) and differential scanning calorimetry (DSC), which results in confirmation of secondary crystallization in the heat treatment process. The effect of heat treatment on the structure and morphology of PBO fiber's surface was investigated with X-ray photoelectron spectroscopic analysis (XPS), scanning electron microscopy (SEM) and atomic force microscopy (AFM). The results show that heat treatment not only has an effect on the composition of PBO fiber's surface, but also improves the microstructure of PBO fiber, makes fiber more regular.