Self-assembly of block copolymers (BCPs) in microfluidic chips is a versatile yet effective route to produce micellar aggregates with various controllable sizes and morphologies. In this study, the morphological transformation of the BCP of polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) assemblies from irregular aggregates to multicompartment micelles and ultimately to ordered spherical micelles is demonstrated in microfluidic chips. Our experimental and computational simulation results indicate that the transverse diffusion of solvents plays an important role in the morphological transformation of PS-b-P4VP assemblies in the confined flow condition. We find that the mixing time (t(mix)) between a BCP/tetrahydrofuran (THF) solution and water affects the morphological transformation. Micellar morphologies are intended to transform from aggregates to ordered spherical structures under a relatively long mixing time (t(mix)). In addition, it is observed that the size of the micelles decreases with the increase of the flow velocity ratio by tuning the hydrodynamic conditions of the flows. Moreover, by adjusting the initial polymer solution concentration, temperature, and weight fraction of the introduced homopolystyrene (hPS), which can affect the viscosity of the BCP solution, the flow diffusion in the microfluidic chip and the resulted micellar structures can also be readily adjusted. The current study provides a new flow-driven method to adjust the micellar ordered structural transformation under the nonequilibrium state.