Targeted at improving overall hydro-thermal performance of microfluidic cooling, a novel embedded cooling configuration using gradient distribution micro pin fin arrays (GD-MPFA) is proposed. A moderate porosity range and fin diameter range are recommended by the optimization of theoretical and numerical 3D fluid-solid conjugate heat transfer simulations. To reveal the hydro-thermal characteristics and advantages of the GD-MPFA, the comparisons between the GD-MPFA and the uniform micro pin fin arrays design (U-MPFA) were made with different coolants. For coolant of DI Water and HFE-7100, GD-MPFA design demonstrates a step-rising and periodical-varying trend of temperature respectively, obviously eliminating maximum temperature difference. However, using a dielectric coolant (HFE-7100) exacerbates thermal management challenge with obviously increasing peak temperature. Therefore, a further investigation is still needed to low peak temperature and temperature difference for dielectric coolant at a higher heat flux under an acceptable pumping power.