The invention relates to a method for determining a fatigue weak area of a stirring friction welding joint considering microstructure inclusion and crystal orientation. The method comprises the following steps: cutting a tiny test piece of each area of a joint, and performing data processing to obtain the static load mechanical property and the fatigue parameter under a cyclic load; performing grinding, polishing and electrolysis sequentially to the tiny test piece cut from each area; obtaining a cyclic stress-strain curve of each area inclusion by a mixing formula in combination with the cyclic stress-strain curve of each area of the joint; establishing a microstructure gradient model of the stirring friction welding joint for each grain in the representative volume element given by different orientation attributes, wherein a nonlinear motion hardening model is adopted for the material of a macro model; applying a fatigue load to the model; observing the stress-strain distribution condition of each area of the joint, and emphatically analyzing the stress-strain distribution conditions at the grain boundary of multiple grains, of the grains different in orientation and near the inclusion in the representative volume element, wherein the relatively obvious local stress concentration area and the relatively great-strain area are fatigue weak areas.