Mycobacterium tuberculosis (Mtb), is the main pathogen causing tuberculosis (TB). Autophagy is an important regulatory pathway to eliminate intracellular Mtb. However, how Mtb escapes autophagy clearance remains largely unclear. Here, we found that microRNA-25 (miR-25) expression was significantly upregulated in the lung tissues of mice infected with Bacillus Calmette-Guerin (BCG) and macrophages infected with Mtb or BCG, especially in the early stages of infection. MiR-25 can significantly increase the survival of Mtb and BCG in macrophages. We validated that miR-25 targets the NPC1 protein located on the lysosomal membrane, resulting in damage to lysosomal function, thereby inhibiting autophagolysosome formation and promoting the survival of Mtb and BCG. Consistently, mice lacking miR-25 exhibited more resistant to BCG infection. In addition, we found that Rv1759c induces the expression of miR-25 through NFKB inhibitor zeta (NFKBIZ). Together, we reveal a new mechanism by which Mtb regulates NPC1 to influence lysosomal function and increase the survival of Mtb through the autophagy pathway, providing an early biomarker for TB infection and a new treatment strategy against TB.