A 3D transient model was established based on the theories of fluid dynamics and heat transfer to analyze the fluid flow and the heat transfer characteristics in the liquid pool when a pulse laser was used to weld the Hastelloy C-276 alloy. On the basis of software Fluent, the Finite Volume Method (FVM) was employed to solve the control equations and the algorithm of SIMPLE was adopted to deal with the coupling of velocity and pressure. The Pe number was induced to evaluate the relative importance of convection and conduction then to analyze the heat transfer characteristics of welding pool. The research indicates that fluid flow velocities along the welding direction in the liquid pool increase with the increasing of the distance from the melting pool center, and then decrease. Under the given conditions, the maximum flow velocity is firstly found at the 0.2 mm from the melting pool center, then it reduces to zero rapidly and velocities in front of the melting pool along the welding direction are slightly larger than that of in the rear ones. Furthermore, The convection leads the melting pool to wider and shallower and the interaction of convection and conduction decides the final weld joint morphology. The numerical simulation is in good agreement with the experimental results, Which proves that the model can provide a theoretical basis for the analysis of the fluid flow in the weld pool during pulsed laser welding thin Hastelloy C-276 alloy.