A high-aspect-ratio microchannel heat exchanger based on multi-tool milling process was developed. Several slotting cutters were stacked together for simultaneously machining several high-aspect-ratio microchannels with manifold structures. On the basis of multi-tool milling process, the structural design of the manifold side height, microchannel length, width, number, and interval were analyzed. The heat transfer performances of high-aspect-ratio microchannel heat exchangers with two different manifolds were investigated by experiments, and the influencing factors were analyzed. The results indicate that the magnitude of heat transfer area per unit volume dominates the heat transfer performances of plate-type micro heat exchanger, while the velocity distribution between microchannels has little effects on the heat transfer performances.