Reduced activation ferritic/martensitic (RAFM) steels are among the most competitive candidates of structural materials for nuclear fusion reactors, due to their superior comprehensive properties. Friction stir welding (FSW) was investigated in joining RAFM steel, considering its potential advantages in obtaining an optimal microstructure and mechanical properties of welded joint. To evaluate the feasibility of FSW in joining RAFM steel, an in-depth understanding of the microstructure-property relationships for friction stir welded joints of RAFM steel is necessary. In this research, the quantitative relationships between microstructural evolution and tensile properties in the stir zone (SZ) of friction stir welded RAFM steel after post-weld tempering treatment (PWTT) were systematically studied. Three different post-weld tempering temperatures namely 720 °C, 760 °C, and 800 °C were adopted. Then the uniaxial tensile properties were tested at room temperature and 550 °C, respectively. Electron backscatter diffraction (EBSD), transmission electron microscopy (TEM), and the Thermo-Calc Calphad software were adopted to systematically investigate the microstructural evolution. Martensite lath width, precipitate number density, equilibrium solid solubility of alloying elements in the matrix, and geometrically necessary dislocation (GND) density were analyzed quantitatively. With the results obtained, we assessed the contribution of each strengthening mechanism to the 0.2% offset yield strength. According to the effective inter-barrier spacing theory, a microstructure-sensitive yield strength model was obtained to well predict the change in yield strength at different conditions. Finally, the results calculated by equivalent strengthening effect indicated that the crucial microstructure determining the yield strength of the SZ for RAFM steel after PWTT is the high density of dislocation substructures.