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The present study was focused on the investigation of effect of defects on the CNT thermal performance. In order to investigate effect of defects on the material properties of the CNT, MD models were built using the Materials studio software (Accelrys, Inc). In this study, a series of MD models were built to simulate the effect of defects on thermal performance of the SWCNT. Based on Fourier's law, thermal conductivities of the SWCNT with different kinds of defects were calculated. The MD simulation results showed that defects in the CNT had heavily effects on thermal conductivity of SWCNT. The thermal conductivity of SWCNT was drastically reduced by those defects. This MD simulation gave a basic understanding of the effect of defects on material performance of CNTs and provided information for the future study.