In this article, the thermal and frictional characteristics of interrupted wavy mini-channel are experimentally investigated as the wavy vortex generator miniature channel (WVGMC) using SiO2–H2O and Al2O3–H2O nanofluids. Its performance characteristics are compared to the common configurations of cooling mini-channels, that is, the wavy mini-channel (WMC), straight mini-channel (SMC), and the miniature channel. The effect of the geometric shape of mini-channels, mass flow rate, coolant fluid type, and the concentration of nanoparticles on the thermal and hydraulic performance inside the different geometries are investigated. The range of Reynolds number and weight fraction of nanoparticles are considered to be 500–2000 and 0–0.3 wt%, respectively. The results show that the highest Nusselt number and overall performance are obtained in the WVGMC for all coolant fluids. The Nusselt number is improved about 27.5%, 22%, and 26.5% for the distilled water, SiO2–H2O nanofluid, and Al2O3–H2O nanofluid in the WVGMC compared to WMC, respectively. Also, the friction factor is increased in the WVGMC; for example, this enhancement rate is about 8.2% for the water flow compared to WMC. The SMC show the least Nusselt number for both nanofluids. In all geometries, the thermal performance is increased using the nanofluids than that for the deionized water. Thus, the WVGMC is suggested as an efficient geometry to design the cooling mini-channels.