Emulsification-induced assembly is employed to allow structural diversity in nanoaggregates of a biocompatible amphiphilic polymer, poly(ethylene oxide)-block-poly(ε-caprolactone). Onion-like vesicles are efficiently produced by tuning the interfacial instability of the oil-in-water emulsion. The increase in the polymer concentration and use of the organic solvents with a low interfacial tension between water and the oil phase lead to a strong tendency of emulsion droplets to generate the onion-like vesicles. The vesicular networks and fibers are also obtained by controlling the concentration and type of the surfactant, respectively. Interestingly, the onion-like vesicles composed of alternating walls and water channels and the vesicular networks originated from a string of vesicles show dual-loading ability for hydrophobic and hydrophilic dyes but slightly different loading capacities. This result indicates that the development of a methodology to fabricate well-defined, unique nanostructures, such as multivesicular and multilamellar nanostructures, and subsequent elucidation of their structure-property relationships can provide useful guidance in the design of novel biomedical materials.