In this paper, numerical investigations are presented for hybrid nanoparticle migration and free convection heat transfer of two kinds of nanofluids in a micromixer at the fixed propeller condition. The inner blades and outer crust of the micromixer are kept at constant hot and cold temperatures, respectively. Two kinds of hybrid nanofluids, TiO2‐CuO water and ethylene glycol‐(MoS2‐SiO2), are considered. The governing equations including velocity, pressure, temperature formulation, and nanoparticle concentrations are solved by a partial differential equation solver based on the Galerkin finite element method. The results are discussed based on the governing parameters, such as nanoparticle volume fraction, thermal and solutal Rayleigh numbers. The average Nusselt number was found to increase with the increasing nanoparticle volume fractions. Also, increasing the thermal Rayleigh number enhanced heat transfer while the solutal Rayleigh number has an insignificant effect on it. More importantly, increasing the thermal Rayleigh number assisted avoiding the agglomeration of nanoparticles around the blades and ensured more uniform nanoparticle distribution.