The modified 9Cr-1Mo steel was selected to conduct friction stir welding experiment. Defect-free welded joints were successfully obtained with the welding parameters of 300rpm-50mm/min and 400rpm-50mm/min. The microstructures of the welded joint were observed by scanning electron microscopy, electron backscatter diffraction and transmission electron microscope. The main microstructural characteristics of the weld zone (WZ) and the high-temperature heat affected zone are the formation of fresh quenched martensite, dissolution of M23C6 carbides, grain refinement and increase in kernel average misorientation. The WZ is significantly hardened, and the maximum hardness of this region is about twice that of the base material (BM). The ultimate tensile strength of the welded joint is up to 98% that of BM. The absorbed impact energies of the SZ and HAZ reach 77.8% and 87.4% that of the BM, respectively. Besides, the influence of post weld heat treatment on the microstructure and mechanical properties of the welded joint was also investigated.