Addition of a vortex generator (VG) to the heated surface creates longitudinal vortices in the flow; however, it induces drag. Surface modification of the VG may play a role in the thermal performance of the system. Therefore, flow and thermal behavior are studied for a secondary surface (SS) attached to the primary surface of a rectangular VG, which is placed inside a rectangular channel using air at Re = 5000. The VG with the SS is compared with a conventional rectangular VG having volume constant. With the addition of SS, the flow behind the VG greatly shears the produced primary vortex (P), which results in stretching. Stretching increases the angular momentum of the vortex with the decrease in the span of the produced vortices. The interaction between the co-rotating vortices P and high pressure side horse-shoe vortex (Hp) shows that the higher strain field induced by the vortex P shears away the vortex Hp. The vortex P developed under the influence of SS induces a higher degree of tilting toward the heated surface with low propagation speed. Finally, the dynamic decomposition of the vortices in the channel reveals that the vortex P appears to be dominant.