The occurrence of heat transfer deterioration (HTD) in supercritical pressure boilers, where the wall temperature rises abruptly is an undesirable phenomenon that is limiting the design of new promising engineering applications. This may cause operational problems such as tube burnouts which could result in a catastrophic system failure. Understanding ways of eliminating HTD is of great importance for the design of safe and reliable supercritical pressure boilers. In this paper, vortex generators (VGs) are installed in circular and annular channels to investigate HTD phenomenon of supercritical water flowing upward at high heat flux and low mass flux using shear stress transport (SST) k - ω turbulence model in ANSYS-FLUENT. Results on wall temperature distribution for the smooth and enhanced channels are compared with available experimental data, and good agreements are obtained. The effects of VG’s size, position, and number on HTD are investigated. The results indicate that VG’s size slightly suppresses and delays HTD downstream of the VG, and there exists an optimum size beyond which HTD starts to aggravate. A strong effect of VGs on heat transfer coefficient (HTC) profiles is observed at locations where VGs are installed and at the downstream locations, with the normalized HTC showing that the wall temperature oscillates a couple of times before becoming stable once the flow returns to fully developed state. The VG’s position has the most significant effect on HTD for any single VG. Increasing the number of VGs installed in-line at the start of the major peak baselines significantly suppresses and delays the peak. Mechanism analysis based on radial distributions of velocity and turbulent kinetic energy (TKE) at different axial positions of both channels shows that HTD suppression is caused by the weakening of the buoyancy effect due to increased TKE near the wall downstream of the VG, whereas the delay is caused by the boundary layer recovery effect due to flow redevelopment after being disrupted by the VG.