Heat transfer enhancement in parallel plate-fin heat exchanger is examined by performing three-dimensional numerical simulations of longitudinal vortex generators (VG) with protrusions. The turbulence is modeled using the shear-stress transport (SST) κ-ω model and validated with correlations and experimental data at Reynolds number equal to 4600. Hemi-spherical protrusions are inserted downstream two VG configurations: delta winglet type (DWP) and a new VG configuration named inclined projected winglet pair (IPWP), in various locations, leading to the definition of six different configurations. Based on the streamwise distribution of Nusselt number and friction coefficient criteria in addition to vorticity, the local performance is analyzed. Some VGs with protrusions are examined and show better performance relative to VGs standing alone. The present study highlights the different mechanisms involved in the convective heat transfer intensification by generating multiple interacting vortices while adding protrusions with low pressure drop penalty. Finally, it is found that the IPWP with protrusions, set downstream in the middle, bestows the best global performance with about 7.1% heat transfer enhancement compared to DWP configuration.