Botrytis cinerea infection of grape berries leads to changes in the chemical composition of grape and the corresponding wine and, thus, affects wine quality. The metabolic effect of Botrytis infection in Champagne base wine was investigated through a (1)H NMR-based metabolomic approach. Isoleucine, leucine, threonine, valine, arginine, proline, glutamine, γ-aminobutyric acid (GABA), succinate, malate, citrate, tartarate, fructose, glucose, oligosaccharides, amino acid derivatives, 2,3-butanediol, acetate, glycerol, tyrosine, 2-phenylethanol, trigonelline, and phenylpropanoids in a grape must and wine were identified by (1)H NMR spectroscopy and contributed to metabolic differentiations between healthy and botrytized wines by using multivariate statistical analysis such as principal component analysis (PCA). Lowered levels of glycerol, 2,3-butanediol, succinate, tyrosine, valine derivative, and phenylpropanoids but higher levels of oligosaccharides in the botrytized wines were main discriminant metabolites, demonstrating that Botrytis infection of grape caused the fermentative retardation during alcoholic fermentation because the main metabolites responsible for the differentiation are fermentative products. Moreover, higher levels of several oligosaccharides in the botrytized wines also indicated the less fermentative behavior of yeast in the botrytized wines. This study highlights a metabolomic approach for better understanding of the comprehensive metabolic influences of Botrytis infection of grape berries in Champagne wines.