A process for preparing the drug-loaded cyanoacrylate nanoparticles is described. The cyanoacrylate nanoparticles which effectively deliver biological and therapeutic agents are synthesized by miniemulsion polymerization with surfactant, pluronic F127 or F68. Before initiation of polymerization, active agents with particularly highly hydrophobicity are dissolved in cyanoacrylate monomer. Compared with the drug-loaded polyalkylcyanoacrylate nanoparticles produced by emulsion polymerization, those produced by miniemulsion polymerization possess higher loading and encapsulation efficiencies. While the content of dissolved agents increases, furthermore, the loading and encapsulation efficiencies increase concurrently.