The utilization of punched vortex generators has been established as an effective means to enhance heat transfer in heat exchangers. However, there are few studies on the use of perforated rectangular winglet pairs in heat exchange tubes and the study of perforation parameters based on this approach in the existing literature. In this paper, three parameters, including three height ratios, four perforation indices, and three pitch ratios, are considered experimentally and numerically. In the Reynolds number range of 7454–13,664, the effects of perforated rectangular vortex generator pairs on fluid flow and heat transfer are obtained by scaling parameters such as Nusselt number ratio, friction factor ratio, thermal enhancement factor, field synergy number, entropy generation, and exergy efficiency. The numerical results indicate that the perforation will lead to a reduction in turbulent kinetic energy in the local multi-longitudinal vortices on the rear side of the vortex generator, resulting in a decrease in local heat transfer as well as friction loss. Meanwhile, the pitch of perforated rectangular vortex generator pairs plays a crucial role in heat transfer and friction loss, enabling an increase in the Nusselt number of smooth tubes by 68–257%. Furthermore, the results are proved using the principle of entropy generation and exergy efficiency analysis. As Reynolds number increases, the thermal enhancement factor gradually decreases. Notably, the maximum thermal enhancement factor of 1.43 is achieved when the Reynolds number is equal to 7454, the height ratio is 0.08, the perforation index is 0.18, and the pitch ratio is 1.04.