A new cyclotriphosphazene derivative substituted by tryptophan ethyl ester groups, namely, hexa-[p-(carbonyl tryptophan ethyl ester) phenoxy)] cyclotriphosphazene (HEPCP), was synthesized. The nanoparticles self-assembled from the hydrophobic HEPCP were prepared by a facile desolvation method. The nanoparticles were characterized by SEM, TEM, FTIR, XRD, TGA, CLSM and fluorescence spectrum. Based upon the molecular conformation of HEPCP and the spatial arrangements of side substituent groups, a growth mechanism was proposed for the formation of the nanoparticles. The obtained nanoparticles were highly thermally stable and exhibited strong fluorescent emission, and could be potential candidates for drug-loading carriers and tracer drug delivery.