Multicompartment micelles (MCMs) attracted much attention since they have subdivided domains that could be employed to encapsulate and transport diverse compounds simultaneously. Usually, preparation of MCMs relied on precise synthesis of block copolymers (BCPs) and elegant control of assembly kinetics, making it difficult to successively produce MCMs. Herein, we report a facile yet effective method for preparing MCMs by adjusting the hydrodynamics in microfluidic channels. It was found that well-defined MCMs were formed through hydrodynamics-dependent secondary assembly in microfluidic chips. By adjusting the flow diffusion process by varying the flow rate ratio and total flow rate, both the internal structure and size of MCMs could be effectively changed. A product diagram of micellar morphologies associated to the initial polymer concentration and flow rate ratio of water/BCPs solution was constructed. More interestingly, quantum dots (QDs) could be selectively loaded into different domains of the MCMs. Consequently, the Förster resonance energy transfer among QDs could be effectively suppressed. Thus, the emission spectrum of MCMs/QDs hybrid particles could be easily tuned by changing the ratio of QDs, showing great potential application in photonics and sensors.