Smart flanges are used for pipeline and riser repair in subsea. In a typical case in the gas export pipeline project, the end cap bolts of a 4inch smart flange were broken during operation, and in turn leakage occurred. This work presents the detail of three dimensional finite element analysis of the smart flange to support the observed end cap bolts failure. From finite element analysis it turns out that in the presence of external bending moment, an uneven contact distribution is present between seal and end cap, which in turn changes the uniform load distribution on bolts and threaten the integrity of bolts. On the other hand, 3D finite element analysis of interaction between pipeline and seabed is presented by means of Abaqus to explore the distribution of bending moment along the pipeline route. It is found that lateral buckling occurs in the pipeline which introduces large bending moment.