By numerical simulation computation, after passing the pulsating flow, enhanced heat transfer mechanism in spirally fluted tubes was researched. Numerical result shows that pulsating flow can cause the outlet pressure to fluctuate cyclical and the extent of fluctuation increases with the pulsating flow frequency. The pulse flowing can make the fluid generate the whirlpool nearby the spirally fluted tubes and the phenomenon of periodic production, drift, and fall-off appears. Because of the vortex, the fluid motion and relative motion are enhanced. The pulse flowing can improve the coordination level between velocity and temperature, thus has strengthened the heat transfer effect.