For the sake of design and integrity assessment of the fracture toughness of high-grade pipelines, it is necessary to carry out accurate fracture toughness assessment of the welded joints. The study of more concise and effective fracture toughness testing methods has important theoretical and engineering value. At present, the fracture control of girth welding joints is mainly based on J integral, CTOD and CTOA. However, it is hard to carry out standard fracture toughness tests at some local narrow areas of the welded joints such as the heat affected zone for the difficulty of sampling. On this basis, this paper aims to propose a method to determine the fracture initiation toughness JIC of the welded joints of high-grade pipeline steels based on the micro-sample test method - small punch test. Firstly, small punch specimen with through-thickness notch was designed. Secondly, the finite element model of the notched specimen was established, and verified by the notched specimen tests of X80 steel. Furthermore, the elastic–plastic material properties of different zones of the welded joint were obtained by the empirical correlation method of small punch test and further used for the determination of J contour integral. The GTN damage parameters were calibrated by the three-point bending tests and further used for the determination of the crack initiation displacement. Finally, the fracture initiation toughness JIC(SPT) of different zones of the welded joint were obtained by the SPT method and verified by the three-point bending test. The results show that the fracture initiation toughness JIC(SPT) of each region of the welded joint obtained by notched SPT specimen were all less than the SENB test results. But there is a good empirical correlation between the two results so that the SPT method can be further modified by establishing an empirical correlation model. The SPT method has good engineering application prospect for the accurately characterization of the different distribution of fracture toughness in different areas of the welded joints.