A molecular dynamics simulation of the mechanisms responsible for the atomic migration and neck growth during the sintering process remains significant due to the nanoparticle size and the vacancy defect in the Fe structure. In this work, we have designed five sets of single Fe nanoparticles with different vacancy concentrations (0%, 2.5%, 5%, 7.5%, and 10%), which were used to investigate the melting and sintering processes. The existence of the vacancy introduced a vacancy proliferation mechanism, which later reduced the bonding energy of the surface atoms and made the surface diffusion easier. As a result, the melting and sintering temperatures slightly reduce according to the vacancy concentration. Atomic vector diagrams and root mean square displacement have been employed to describe the law of atomic motion; common neighbor analysis and coordination analysis have been used to investigate the structural changes within nanoparticles. The consistent results reveal the influence of vacancy defects on the melting and sintering of nanoparticles and provide a new method to reasonably control the sintering process.