Lysosomal dysfunction caused by abnormal lysosomal ion channels is an important factor leading to neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Lysosomes ion channels regulate lysosomal ion homeostasis, lysosomal membrane voltage, and lysosomal acidity. Structural or functional defects of lysosomal ion channels will cause lysosomal degradation dysfunction, leading to the occurrence and development of neurodegenerative diseases. In this review, The role and mechanisms of various lysosome ion channels in regulating lysosomal function were summarized.The underlying mechanism of the deficits of the ion channels in neurodegenerative diseases were also introduced. Regulating ion channels to improve lysosomal function and promote the clearance of abnormal aggregated proteins are underlying targets for the treatments of neurodegenerative diseases.