Here, we report a novel method to synthesize multifunctional nanoparticles that can be used in biological studies, such as in cell imaging and as a carrier for biomolecules/drugs. The nanoparticles were prepared either via Cu-catalyzed or cucurbit[6]uril (CB6)-catalyzed click reactions between azide groups containing hydrophobic blue, green and yellow emitting fluorene-based conjugated polymers and a hydrophilic diaminodialkyne containing cross-linker. Through the click reaction, not only does the cross-linking confer stability, but it also introduces functional groups, such as triazoles and amines, to the nanoparticles. Moreover, CB6 not only acted as a catalyst to facilitate the copper-free click reaction, but it also allowed us to obtain nanoparticles containing rotaxanes in which the triazole units were encapsulated by CB6 units. TEM images of the nanoparticles also showed that they display very interesting morphologies. Incorporation of hydrophilic functional groups to the hydrophobic conjugated polymers resulted in a distinct phase separation, producing Janus-like or patchy particles.