High-frequency mechanical impact (HFMI) post-treatment is a proven method to improve the fatigue life of welded structures. The positive effects of HFMI treatment are influenced by the weld toe geometries and residual stresses. This study investigates the effect of geometric and mechanical improvements by HFMI treatment on fatigue strength with explicit consideration of the weld toe magnification factor. General fatigue life estimation method is based on experiment data, and residual stress may be considered in addition. In terms of HFMI-treated structures, geometric improvement also affects the fatigue life. Thus, a more efficient method is suggested by considering the weld toe magnification factor to assess the effects of HFMI treatment. First, the weld toe magnification factor in HFMI-treated conditions is calculated to consider the geometrical effect of HFMI treatment at the weld toe region. Second, a stress ratio model is introduced to consider the compressive residual stress by HFMI treatment based on the Paris equation. The results were validated by comparing them with the estimated fatigue life from previous studies on HFMI-treated welded specimens.