Recently waste heat recovery has an important presence into our daily applications. Thermoelectric generators present a possible way to harvest waste heat and make a contribution to energy sustainability. In this study a thermoelectric generator module employed along the chimney which is used to collect the waste heat recovered from the combustion flue gases of almost 330°C. In order to enhance the thermoelectric generator performance, a water-cooled micro heat sink is integrated to the system. A CFD Numerical model using ANSYS-Fluent was used to predict the flow field and heat transfer through the micro heat sink. Additionally, by using the Fluent User Defined Functions (UDF) the thermoelectric generator performance was also predicted where the thermal-electrical fields solved simultaneously. The results showed the effect of applying parallel microchannels and the effect of changing the flow characteristics on the output power of the thermoelectric generators. The proposed system efficiency increasingly improved with the applying of microchannel heat sink. The effect of applying multiple micro heat sink configurations are also presented. The results corroborate previous experimental and theoretical studies.