The effect of carbon deposits on the reactor wall during the growth of multi-walled carbon nanotube (MWCNT) arrays was studied. It was found that the carbon deposits were helpful in converting the continuous catalyst film into carbon-containing nanoparticles before growth started, which was beneficial for the nucleation of MWCNT arrays. As a result, MWCNT arrays synthesized in a reactor with carbon deposits were well aligned with high nucleation density. Further study revealed that this effect could be probably ascribed to some activated species adsorbed in the carbon deposits. These results will be helpful in the repeatable synthesis of high quality MWCNT arrays and in understanding the nucleation process of MWCNT arrays.