In the present study, the enhanced heat transfer performance and mechanism of two types of special-shaped tubes (transversely corrugated tubes and helically corrugated tubes) used in the intermediate heat exchanger of a high temperature gas-cooled reactor are investigated using three-dimensional numerical simulations. The results show that when the dimensionless corrugation height (e/d) and dimensionless corrugation pitch (p/d) are the same, the transversely corrugated tubes have better enhanced heat transfer performance, the Nusselt number is increased by up to 85%; The helically corrugated tubes have better comprehensive performance, the PEC is up to 1.08. The enhanced heat transfer mechanism of the two special-shaped tubes is that the corrugation enhances the turbulent pulsation of the fluid, and the enhancement effect of the transversely corrugated tube is more effective.