Polymer nanostructures can be designed with tailored properties and functions by varying their shape, chemical compositions, and surface functionality. The poor stability of these soft materials in solvent other than water can be overcome by introducing cross-links. However, cross-linking complex morphologies remains a challenge. Here, by using the temperature-directed morphology transformation method, we show that the symmetric (nanoworm) and asymmetric (tadpole) nanostructure cores can be UV-cross-linked through the coupling of styrene and para-chlorostyrene units found in the core by irradiating at 254 nm for up to 5 h. Once cross-linked, these nanostructures maintain their structure in organic solvent, further allowing us to couple on a water-insoluble pro-fluorescent probe with high efficiency.