The objective of this article is to analyze complex micro-channels with wire-net and S-shaped perturbators and implement a reduced order modeling (ROM) approach to assess the entire heat exchanger performance and validate through experiments. Shifting the critical Reynolds number to lower values using perturbators decreases the pressure losses and enhance the thermal efficiency. There is an optimum mass flow (for both perturbators) where the thermal efficiency reaches maximum. The thermal efficiency of the wire-net perturbator is relatively high compared to S-shaped perturbators. The S-shaped perturbators induces strong wall-normal velocity fluctuations and enhances the heat transfer. Furthermore, the turbulence production term provides a deeper insight into flow attachment and detachment near the wire net intersections. The computational fluid dynamics approach (conjugate heat transfer models and ROM) was introduced to reduce the computational grid size and predict the collector performance. The secondary collector performance is determined by considering the microchannels as porous mediums. Apparently, the primary collector performance is determined by considering both secondary collectors and microchannels as porous mediums. The cylindrical secondary collectors contribute nearly 40–50% of the pressure drop. Experimental validation showed that the ROM predicts the heat exchanger performance with a good (<4.4%) accuracy.