Assembly of nanoparticles as interfacial stabilizers at oil-in-water (O/W) interfaces into microscopic suprastructures for stabilizing Pickering emulsions is an intriguing focus in the fields of chemical industry and material sciences. However, it is still a major challenge to assemble nanoscale suprastructures using nanoparticles as building blocks at O/W interfaces for fabricating nanoscale emulsion droplets with applicable potential in nanomedicine. Here, we show that it is possible to fabricate the nanodroplets by assembling highly deformable nanogels into the nanoscale suprastructures at spatially confined O/W interfaces. The compressed assembly of the nanogels induced the formation of the nanoscale suprastructures upon energy input at the nanoscale O/W interface. The hydrogen bonding interaction between the nanogels at the O/W interface are possibly responsible for the stabilization of the nanoscale suprastructures. The nanoscale suprastructures are further employed to stabilize the paclitaxel-loaded nanodroplets, which are found to provide sustained release of the drug, enhanced in vitro cytotoxicity, and prolonged in vivo blood circulation. Furthermore, the tissue distribution and antitumor efficacy studies show that the nanodroplets could induce a higher drug accumulation at the tumor site and enhance tumor growth inhibition when compared with the commercial product. This approach provides a novel universal strategy to fabricate nanoscale suprastructures for stabilizing nanodroplets with built-in payloads using deformable nanoparticles and displays a promising potential in nanomedicine.