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Hypothesis The microfluidic technology can drive molecules to organize into aggregates with nano-structures, and gives a possibility to control aggregate morphologies by adjusting hydrodynamic parameters of microfluidics. COMSOL Multiphysics is a useful software to simulate the mixing situation of solutions in microfluidic. Here, experiments and simulation are combined to study the self-assembly of gradient copolymers in the microfluidic device. Experiments Fluorinated gradient copolymers self-assembled in a three-dimensional co-flow focusing microfluidic device (3D CFMD). Hydrodynamic parameters of 3D CFMD were adjusted to control morphologies and the sizes of copolymer aggregates. A simulation software, COMSOL Multiphysics, was used to simulate the mixing and diffusion of outer phase stream and inner phase stream to explore the mixing kinetics of two streams in the microchannels. Findings 3D CFMD offered a novel platform for the continuous and controllable self-assembly of fluorinated gradient copolymer. Various morphologies of copolymer aggregates were obtained in 3D CFMD, but just spherical micelles were formed by a traditional solvent-inducing method. The flow velocity, initial water content of outer-phase stream, and the copolymer concentration of inner-phase stream had great effects on the morphology and size of copolymer aggregates. The simulation results made us a better understanding on the microfluidic self-assembly. [ABSTRACT FROM AUTHOR]