Recently, X65 carbon steel pipes internally clad with a thin Inconel625 alloy lining are highly used. However, during welding the Inconel625 lining in the root pass, the weld bead is uneven. To avoid weld defects in the successive passes, an additional grinding procedure is always required to flatten the weld bead. It is known that as an indispensable component in GMAW, the shielding gas can protect the liquid metal from oxidation and defects in the atmosphere. The shielding gas composition greatly determines the characteristics of the welding arc which plays a significant role in the heat, mass transfer during welding and flow motion in the weld pool. It is proposed that the uneven weld bead can possibly be improved by changing the shielding gas composition during welding the Inconel625 lining. Therefore, it is necessary to study the effect of shielding gas composition on the weld bead geometry during short-circuit gas metal arc welding (GMAW) of Inconel625 alloy. In this research, short-circuit GMAW of the Inconel625 lining was reproduced in a laboratory scale. Three kinds of gas, argon (Ar), helium (He) and carbon dioxide (CO2) were considered and two types of experimental configurations, bead-on-plate welding and U-shaped groove butt welding were performed. It was found that the shielding gas composition could make a great influence on the arc voltage, power of the heat source (welding arc), flow motion in the weld pool and the resultant geometry of the weld bead. For the Ar-He shielding gas mixtures, the arc voltage is increased as the He content is increased, which is attributed that the ionisation potential of He is higher than that of Ar. As a consequence, with an increase of the He content, the heat source (the welding arc) becomes more powerful and more heat is transferred to the workpiece. A larger fusion area is created. For the Ar-CO2 shielding gas mixtures, it was found that adding 3.3% CO2 to Ar could raise the arc voltage and lead to a more powerful welding arc. More importantly, the presence of oxygen which is dissociated from CO2 can largely reduce the surface tension of the liquid metal. The temperature gradient of the surface tension can be changed from negative to positive and the direction of the Marangoni convection which is driven by the surface tension force will be changed from outward and upward to inward and downward. The efficiency of the heat transfer from the surface of the weld pool to the bottom is greatly enhanced. Consequently, addition of 3.3% CO2 to Ar can deepen the penetration and enlarge the fusion area.