In this paper, based on multi region boundary element method (BEM), a general procedure to calculate stress intensity factors(SIF) of a 3D mixed mode fatigue surface crack is detailed. A BEM model for a welded T joint is constructed referring to the test specimen. The crack corner points are indirectly estimated to circumvent the treatment of the different crack tip singularity at the corner regions. Numerical results from the welded T joint show that this procedure is reliable.