The thermal conductivity of silicon nanowires (SiNWs) is investigated by molecular dynamics (MD) simulation. It is found that the thermal conductivity of SiNWs can be reduced exponentially by isotopic defects at room temperature. The thermal conductivity reaches the minimum, which is about 27% of that of pure 28Si NW, when doped with fifty percent isotope atoms. The thermal conductivity of isotopic-superlattice structured SiNWs depends clearly on the period of superlattice. At a critical period of 1.09 nm, the thermal conductivity is only 25% of the value of pure Si NW. An anomalous enhancement of thermal conductivity is observed when the superlattice period is smaller than this critical length. The ultra-low thermal conductivity of superlattice structured SiNWs is explained with phonon spectrum theory.