The paper presents a micro-fluidics cooling system which is designed on a silicon substrate including a micro-pump, two temperature sensors, a flow sensor and some microchannels. To design the cooling system optimally, a finite element model is built. The temperature distribution on the silicon substrate is analyzed using the model. Moreover, the quantitative relation is given of the temperature distribution, flow velocity and driving capability of the micro pump. Consequently, the structure parameters and design requirements of the cooling system are obtained.