This paper explores the performance effects of a novel small-scale multiple vortex generators (MVG) on heat transfer deterioration (HTD) mitigation and pressure drop using supercritical CO2 (sCO2) as the working fluid. The HTD mitigation and pressure drop are examined using an overall performance factor, R = ΔHTD/(Δp/Δp0). Numerical calculations are first conducted to investigate the effects of single conventional vortex generator's (VG) configurations (rectangular, triangular and trapezoidal). The results indicate that under the same aspect ratio, rectangular VG has the largest area facing the fluid flow and the largest angle of attack which induces the strongest longitudinal vortices leading to its highest value of R. Then, the morphological properties (density and height) of five pairs of evenly distributed rectangular VGs in an MVG are varied while their uniformity is maintained. With the increase in MVG's height, the channel's heat transfer coefficient (HTC) profiles increase significantly at the locations where MVG is installed while the opposite trend is found for R. The density and nonuniformity of the MVG have the highest performance effects on HTD mitigation, with R of more than 18% and 11% for the density of 2.5 and non-uniform MVG respectively. Analysis reveals that as the density of MVG increases, the fluid recirculation zone behind each VG diminishes correspondingly, causing a greater vortex intensity mixing by swirling flows which enhances the downstream production of turbulence kinetic energy (TKE), thus weakening the buoyancy forces and leading to HTD mitigations. In addition, by further increasing the MVG density beyond 2.5, it was found that the HTC decreases while the pressure drop increases, with the wall temperature peaks stabilizing at 178 °C, which demonstrates the breakdown of Reynold's analogy. Increasing the number of VGs in an MVG increases its delay and broadening effects on the wall temperature peaks by further delaying the boundary layer recovery caused by interaction of longitudinal vortices generated by each VG, but has relatively little effects on R. Also, analysis further reveals the presence of buoyancy-induced flow oscillations near the channel walls, which are attenuated by the VG and MVG effects. Overall, MVG offers superior performance than convectional single VGs in terms of HTD mitigation, and the results presented here can be employed as a reference guide in the design of highly efficient, safe and reliable supercritical heat exchanger systems.