The invention provides a pipeline welding seam defect treatment method. The method includes the steps: firstly, performing non-destructive inspection for welding seams; secondly, determining the form of formed grooves according to that defects are positioned inside the welding seams, on outer surfaces of the welding seams or at the roots of the welding seams; thirdly, determining a welding method according to the form of the formed grooves and welding the welding seams; and fourthly, performing post-weld heat treatment for welded joints after welding. By the method, welding seam defects on materials can be directly repaired by welding, 100% of one-step welding qualified rate is not pursued necessarily, process control requirements are lowered, defect inspection before heat treatment can be omitted, pipe replacement is avoided after the defects are caused, and accordingly production cost is reduced greatly.