Mitophagy is a special version of autophagy which eliminates damaged or redundant mitochondria effectively and selectively. Eukaryotes conduct mitochondrial quality control via mitophagy to maintain the function of the power-generating organelles. Recently, a series of studies have demonstrated that two Parkinson’s disease-related genes, PINK1 and parkin, were involved in mitophagy. Parkin and PINK1 cooperate with each other to recognize damaged mitochondria specifically. Particularly, ubiquitin and deubiquitinases play essential roles in modulating parkin activity and mitophagy efficiency. Here we introduce and review the recent studies on PINK1/parkin pathway in mitophagy.