Nanostructures (vesicles, micelles, bilayers) are important in nanomedicine and biochemical processes. They are agents for encapsulation and eventual release of drugs, flavors, and fragrances. The structural transition from micelles to vesicles through disk-like intermediate states has been demonstrated previously. Here, we disclose a new route for the micelle-vesicle transition, where micelles aggregate to first form long tubules that become unstable, and break up into vesicles. A simple theory, based on energy principles, is presented to explain the tubule-vesicle transition. Observation of this new tubular intermediate state has been facilitated by the development of an integrated microfluidic chip/cryogenic transmission electron microscopy (cryo-TEM) unit. Although this transition has been observed in a specific amphiphilic system where micellar solutions of cetyltrimethylammonium bromide (CTAB) and dodecylbenzene sulfonic acid (HDBS) are mixed to form vesicles, this new tool can be applied broadly to study transient structures in nanoscale systems under the very controlled conditions provided by microfluidics.