Flow characteristics and heat transfer performances of carboxymethyl cellulose (CMC) aqueous solutions in the microchannels with flow control structures were investigated in this study. The researches were carried out with various flow rates and concentrations of the CMC aqueous solutions. The results reveal that the pin-finned microchannel has the most uniform temperature distribution on the structured walls, and the average temperature on the structured wall reaches the minimum value in cylinder-ribbed microchannels at the same flow rate and CMC concentration. Moreover, the protruded microchannel obtains the minimum relative Fanning friction factor f /f 0 , while, the maximum f /f 0 is observed in the cylinder-ribbed microchannel. Furthermore, the minimum f /f 0 is reached at the cases with CMC2000, and also, the relative Nusselt number Nu/Nu 0 of CMC2000 cases is larger than that of other cases in the four structured microchannels. Therefore, 2000 ppm is the recommended concentration of CMC aqueous solutions in all the cases with different flow rates and flow control structures. Pin-finned microchannels are preferred in low flow rate cases, while, V-grooved microchannels have the minimum relative entropy generation S'/S 0 ' and best thermal performance TP at CMC2000 in high flow rates.