Spinal muscular atrophy (SMA) is a progressive neuromuscular disease, associated with motoneuron loss and muscle wasting. Numerous SMA-causative mutations have been reported in survival motor neuron (SMN) gene(s); however, the pathogenic mechanism underlying SMA remains unclear. In the present study, we showed that SMN modulates the expression of transcription factor EB (TFEB), a master regulator of lysosomal genes that plays a key role in lysosome function, autophagy, and the mammalian target of rapamycin (mTOR) signaling pathway. The transfection of small interfering RNA (siRNA) targeting SMN caused a reduction in TFEB expression in the motoneuron-like NSC-34 cell line. In differentiated NSC-34 cells, either SMN or TFEB knockdown resulted in reduced lysosomes at neurites and the atypical accumulation of swollen and enlarged lysosomes in cell bodies. SMN knockdown caused the reduced expression of lysosome-related genes, resulting in the decline of lysosomal degradation and increased autophagic flux. These SMN-depletion-induced aberrations in lysosomes and autophagy could be rescued by the exogenous expression of TFEB. Furthermore, SMN depletion in NSC-34 cells resulted in the decreased phosphorylation of mTOR and its downstream signals. Finally, SMA transgenic mice exhibited reduced TFEB and lysosomal protein expression and the inactivation of mTOR signaling in the lumbar spinal cord at postnatal day 11, compared with their counterparts. These findings indicated that SMN regulates lysosomal gene expression and functions by altering TFEB expression in motoneurons. The targeting of lysosomes might represent a new strategy for the treatment of SMA.