Three different stir tools with the pin eccentricity of 0, 0.4 and 0.8 mm were applied to the friction stir processing (FSP) of Al-6061 alloy. Results show that the pin-affected zone (PAZ) enlarges and the grain size in the stir zone (SZ) decreases as the pin eccentricity increases. Moreover, the low peak FSP temperature induced by the pin eccentricity gives rise to the coarsening of strengthening precipitates in the SZ. Compared with the pin-eccentric FSP samples, the SZ produced without pin eccentricity exhibits the highest hardness and yield strength due to the high amount of fine precipitates. However, the application of pin eccentricity elevates the overall tensile properties of FSP samples through changing the failure location from heat-affected zone (HAZ) to SZ.