Millimeter channel reactors (MCRs) have received increasing attention because of their ability to enhance treatment capacity in addition to the advantages of microchannels. In previous studies, less work has been conducted on the micromixing process and enhancement strategies for non-Newtonian fluids in MCRs. In this study, the micromixing efficiency in MCRs was experimentally investigated using CMC aqueous solution (aqueous carboxymethyl cellulose sodium) to simulate a non-Newtonian fluid, and the enhanced mechanism of micromixing efficiency by the addition of internals and rotation was analysed by computational fluid dynamics (CFD) simulations. The results show that in the conventional channel, increasing the flow rate improves the micromixing efficiency when the CMC concentration is low. However, when the CMC concentration is higher, the higher the flow rate, the lower the micromixing efficiency. The highest micromixing efficiency is obtained for the rotationally coupled inner components, followed by the single rotation and the lowest is for the internals only. CFD simulations reveal that the most effective way to improve the micromixing efficiency of non-Newtonian fluids with shear-thinning behavior is to increase the shear force in the reactor, which effectively reduces the apparent viscosity. These results provide the theoretical foundation for enhancing the micromixing process of non-Newtonian fluids in small-size reactors.