Autophagy is an evolutionary conserved lysosomal degradation pathway which is involved with a variety of cellular process, but the relevant mechanisms remain elusive. Here I find that TM9SF1, a nine-spanning transmembrane protein and human two-pore channels (TPCs) regulate cell autophagy. More importantly, TM9SF1 and TPCs are found in endolysosomal system, and among all TM9SF family, only TM9SF1 interacts with TPC2 structurally, which suggests that there might be functional interaction between TM9SF1 and TPC2. Indeed, my results showed that TM9SF1 increases LC3-II/LC3-I ratio in TPCs knockdown groups significantly compared with groups without TPCs knockdown, which indicates TM9SF1-induced autophagosome formation is dependent on TPCs knockdown. Therefore, it is of great interest to pursue to discover the detailed functional interaction between TM9SF1 and TPCs on cell autophagy, which is associated with a wide range of diseases including cancer, neurodegenerative diseases, heart diseases, diabetes and infections.