The thermo-hydraulic effects of the number and placement of holes in rectangular winglet vortex generators on a solar air heater were investigated numerically. This study examined airflows under conditions where the Reynolds number ranged from 3000 to 20,000 and the Prandtl number was 7.070. Variations in the number of holes, ranging from one to nine, resulted in ten different hole-arrangement patterns. The blockage ratio, which is defined as the ratio between the surface area of the vortex generator and the cross-sectional area of the airflow duct, remained constant throughout the investigation, which made it necessary to vary the hole diameters. For the simulations, the Realizable k-epsilon model supplemented with a wall function was employed. The results indicated that the number of holes had a significant effect on the Nusselt number, and the winglet vortex generator featuring a single hole was observed to have the highest averaged Nusselt number, whereas the nine-hole configuration had the lowest. Conversely, the impact on the friction factor was comparatively minimal. Additionally, an analysis of the hole placement revealed slight variations in the averaged Nusselt numbers and friction factors when the number of holes remained constant. Velocity plots and pathlines were utilized to elucidate the flow structures and induced vortices. This study concludes that large and well-organized vortices were more efficient for heat transfer under the experimental conditions. In addition, maintaining a constant blockage ratio between the vortex generator’s surface area and the airflow duct’s cross-sectional area in the solar air heater contributed to the friction factor being mostly unaffected by the number of holes.