The relationship between protein post-translational modification and autophagy has become a hot topic in recent years. A series of proteins are required to participate in the process of autophagy. Protein acetylation has been demonstrated to emerge as the main regulator to autophagy. In this paper, we reviewed related findings from two perspectives. On one hand, the role of protein acetylation on autophagy has been discussed, mainly including histones, transcription factors and most of enzymes to regulate the level of AcCoA. On the other hand, we presented the advancement with the acetylome profile in the process of autophagy. Acetylase and deacetylase are the main enzymes to be responsible for protein acetylation. The relationship between these enzymes and their substrates merited to be intensively investigated in the future studies. All of data would be very valuable to explore the mechanism with autophagy.