In this research, the 600 MPa acid resistant steel was used as flash butt welding base material, to study the effect of different upset allowance on the microstructure and mechanical properties of the joints. The results can be obtained as follows: with the increase of the upset allowance, it has a significant effect on the elongation, the ferrite content in the heat affected zone increases, and the joint strength first increases and then slowly decreases. When the upset allowance is bigger than 4mm, there are wide and large bainitic ferrites in the coarse grained zone, the joint strength deteriorates sharply. When the upset allowance is 3-4mm, the mechanical properties of the welded sample are the best, the tensile strength is 686-708MPa, the yield strength is 610-636MPa, the elongation is higher than 13.77%. The steel matrix can be strengthened effectively by forming grain refinement and dispersed granular bainite with proper upset allowance. The different hardness distributions of welded joints to display the difference of microstructure in different regions.