The trend of light-weight structures leads to the wide application of high strength steels in engineering structures. When welding high strength steels, under-matched consumables could reduce the cold-cracking tendency, simplifying the preheating process. However, under-matched welds would sometimes make the high strength base metal pointless due to its weak load-carrying capacity. For the purpose of enhancing the fatigue strength of under-matched welded joints, a fracture mechanics-based optimal fatigue design method of under-matched butt-welded joints is proposed in this work. Heterogeneous mechanical features of welded joints, which are not considered in current standards and codes, are incorporated into the optimal design method. The fatigue limit of the high strength parent metal is taken as the design target, which has seldom been reported. HSLA steel Q550, with its under-matched consumable ER70S-6 composed X-shaped butt-welds, is selected for experimental verification. The experimental results indicate that the fracture mechanic based equal-fatigue-bearing-capacity (EFBC) design method established in this work is feasible and could be a valuable reference for the design of practical engineering structures.