It has been found that viscoelastic fluid has evident heat transfer enhancement function in macro scale. But in micro scale, viscoelastic fluid’s flow and heat transfer characteristics are still unknown. In this paper, the heat transfer process of viscoelastic fluid in the microchannel is studied by numerical simulation method. The simulation results show that the maximum heat transfer enhancement of viscoelastic fluid is up to 800%, compared with pure viscous fluid. The viscoelastic fluid has such obvious heat transfer enhancement function because of its strong secondary flow. Laminar sub-layer can be damaged by the strong secondary flow, and thus radial flow generates in laminar sub-layer. The radial flow can increase the interference and mixing effect, and enhances fluid’s turbulence and convection which can enhance heat transfer as a result. So the heat transfer enhancement depends on the intensity of secondary flow which is caused by the second normal stress difference, and it will increase with the raise of the flow rate.