Trimethyltin chloride (TMT) is a potent neurotoxin to cause neurodegeneration, especially in hippocampus. This study aimed to identify dietary components that can effectively attenuate TMT-induced neurodegeneration in humans. The predominant anthocyanin in human diets, cyanidin-3-O-glucoside (C3G, 5 or 50 mg/kg), was given to mice for 16 days, and TMT (2.7 mg/kg) was injected intraperitoneally once on the eighth day. C3G (50 mg/kg) significantly alleviated TMT-induced seizures and subsequent cognitive impairment by ameliorating hippocampal neurodegeneration and synaptic dysfunction. Furthermore, C3G treatment restored glutamate homeostasis in brain and reversed glutamine synthetase (GS) inhibition in reactive astrogliosis and neuroinflammation, which are critical for C3G’s neuroprotective effects. Notably, C3G decreased the lipopolysaccharide, tumor necrosis factor-α, interleukin-6, and interleukin-1β levels in the mice, which potentially by modulating the relative abundance of Atopobiaceae and Lachnospiraceae in the gut. C3G may be a promising and practical dietary component for reducing TMT-induced neurodegeneration.