The functionalization of single-walled carbon nanotubes (SWCNTs) by forming self-assembled supramolecular structure of 10,12-pentacosadiynoic acid (PCDA) on the carbon nanotube wall is reported. PCDA assemblies on SWCNTs (PCDA/SWCNTs) were polymerized by UV irradiation to extensively conjugated polydiacetylene (PDA). PDA/SWCNT was identified by absorption and emission spectroscopy, scanning and transmission electron microscopies (SEM and TEM) and atomic force microscopy (AFM). PDA/SCWNTs showed strong near-infrared (NIR) fluorescence caused by fluorescence resonance energy transfer (FRET) between PDA network and semiconducting SWCNT core. The micro-patterning of biotinylated PDA/SWCNT with FITC-avidin on biotinylated glass surface demonstrated the potential application for a bio-sensing device. Furthermore, the biocompatibility for mammalian cancer cells was tested by viability experiments, which revealed that the PDA/SWCNTs had very low toxicity below 31.3 mg/L in terms of pristine SWCNTs concentration. Also, PDA/SWCNTs inside the cells can be observed by NIR microscopy. This unique modular method of preparation can contribute to diverse functionalities for practical applications in various non-invasive cellular imaging.