Polydiacetylene (PDA) nanocrystals were successfully encapsulated by soap-free copolymerization of styrene monomer and hydrophilic styrene derivative. The resulting polystyrene-encapsulated PDA nanocrystals became almost uniform and spherical and could be arranged conveniently on a patterned substrate using the tapered cell method. These basic processes to fabricate ordered array structure on a substrate are very important toward photonic devices application made up of PDA nanocrystals in the near future. In addition, the formation mechanisms for encapsulation were discussed in detail.