The heat transfer and flow characteristics of the wavy vortex generator inside miniature channel as process intensification are numerically investigated. The optimization of wavy vortex generator is performed using the response surface methodology. The studied geometrical parameters are the position angle (i.e. -60 degrees,-30 degrees, 0 degrees, 30 degrees and 60 degrees), wave amplitude (i.e. 0.5, 0.75, 1, 1.25 and 1.5 mm) and wave length (i.e. 5, 10, 15, 20 and 25 mm). The coolant fluids are MWCNT-H20 and Al2O3-H2O nanofluids which are simulated by Eulerian two-phase model. The volume fraction of nanoparticles and the range of Reynolds number are 0-1 vol.% and 200-1000, respectively. To validate the numerical modeling, an experimental investigation is conducted. The numerical results show that the MWCNT-H2O nanofluid has the highest overall performance. The position angle of 60 or 150 has the best overall performance. By increasing of wave amplitude and reducing of wave length, the thermal performance is improved. Also, by increasing the volume fraction of nanoparticles, the thermal and hydraulic performance of nanofluids is increased. Finally, the optimal designs of the wavy vortex generator miniature channel are proposed and also the correlations are provided to predict the Nu number and f of the nanofluids.