Main Vessel is an important structure used in Reactor assembly that need to be cooled to avoid non uniform Temperature distribution. Main vessel cooling system consists two concentric cylindrical shells attached to inner side of main vessel. This can be achieved by providing a Spillway weir over the outer baffle in the Main vessel cooling system. This paper describes the thermal analysis of Main vessel -roof slab junction in fast reactor .The analysis is done by varying the height of this junction using computational Fluid Dynamics technique. Fluent is the Post processor used for this thermal analysis. The temperature distribution around the surface of spillway profile is analysed for better results.