Pin-fins are employed in 3-D manifold microchannel (MMC) and its thermo-hydraulic performance is experimentally compared to MMC with plate-fins for the first time. MMCs consist of two layers, a microchannel layer and a manifold layer. A microchannel layer is fabricated by chemically etching the pinfins or the plate-fins on the silicon wafer. The geometric parameters of the pin-fins and the plate-fins are both fixed as the porosity of 0.75, the fin thickness (or diameter) of 50 µm and the fin height of 75 µm. Subsequently, a manifold layer, which is an array of impinging slot jets is fabricated on the glass wafer by a double-sided sandblasting process. The manifold layer and the microchannel layer are anodically bonded to form a monolithic heat sink with the total thickness of 1 mm. On the backside of the silicon wafer, a serpentine metal film with the size of 5×5 mm² is sputtered for electrical Joule-heating and thermometry. Experiments are performed using deionized water as the working fluid, with the pumping powers of 0.001 to 0.1 W. The results on MMCs show that the pin-fins improve the thermo-hydraulic performance: up to 25% reduction in the thermal resistance at the fixed pumping power condition. Furthermore, the wall temperature adjacent to the fluid is maintained at about 80°C with the pressure drop of 30 kPa, even at the heat flux of 1200 W/cm². This stems from that MMC with pin-fins has 30% higher heat transfer coefficient and 50% greater surface-to-volume ratio, even with lower pressure drop compared to MMC with plate-fins. This new cooling device may aid in solving critical challenges in the practical use of silicon-based embedded cooling, owing to its remarkable thermo-hydraulic performance and high energy efficiency.