ALS is a devastating motor neuron disease. Protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification has been found to affect the processing of several important proteins implicated in ALS. However, the O-GlcNAcylated proteome remains unexplored during ALS progression. Herein, we probed the dynamic changes of O-GlcNAcylation in SOD-G93A mice, the most widely used animal model for studying ALS pathogenesis. We discovered that the overall O-GlcNAc level is significantly decreased at the disease end stage. Correlatively, a great increase of OGA was observed. By using isoPTOP, a recently reported chemoproteomics strategy, we furthermore reported the identification of 568 high-confidence O-GlcNAc sites from end-stage SOD1-G93A and NTG mice. Of the 568 sites, 226—many of which occurred on neuronal function and structure-related proteins—were found to be dynamically regulated. These results provide a valuable resource for dissecting the functional role of O-GlcNAcylation in ALS and shed light on promising therapeutic avenues for ALS.