Carbon nanotubes are usually made up of 12 C atoms. By adopting the force constant model, the effects of isotope doping with 13 C on the vibrational, optical, and thermal properties of single-walled carbon nanotubes are theoretically investigated, including the phonon eigenmodes and density of states, the Raman scattering spectra, and specific heat. Three types of doping patterns ͑axial stripes, circumferential bands of varying width, and random͒ are studied, in which an emphasis is put on the isotope-nanotube-junctions. Several new effects of the isotope doping in nanotubes have been found, including the confined optical phonon modes due to the spatial separation of isotopes, the red-shift of Raman peaks in general and blue-shift anomaly of the confined LO peaks in specific tube chirality and doping configuration, and the enhancement of the specific heat due to the 13 C-doping. This work provides with a theoretical guide for isotope labeling, which is important for understanding the growth mechanism of the carbon nanotubes.