The influence of different geometric and operating parameters on the effectiveness of counter flow MEMS heat exchangers are studied in this article. The counter flow MEMS heat exchanger is modelled using ANSYS Workbench; only a repeating unit of the MEMS heat exchanger is studied for all cases. The mathematical model consists of the continuity equations, Navier-Stokes equations, and energy equations. The fluid considered for this study is water. The influence of hydraulic diameter, channel spacing, substrate thickness, structural material, and Reynolds number on the effectiveness of MEMS heat exchanger is studied. Studies are done for hot fluid Reynolds number varying between 50 and 500 while maintaining the heat capacity ratio at unity. The hydraulic diameters and channel spacing considered include 100 μm, 200 μm, and 300 μm while the substrate thickness of 250 μm, 500 μm, and 1000 μm are considered in this study The structural material considered for this study include silicon, stainless steel, and glass. The effectiveness is determined using the inlet and outlet temperatures of the fluids. It is found that the effectiveness of the MEMS heat exchanger reduces with increase in Reynolds number. Moreover, increase in hydraulic diameter, spacing and thickness of the MEMS heat exchanger reduces its effectiveness for a specific hot fluid Reynolds number.