Elevated carbon dioxide concentrations can mitigate significant threats posed by high-temperature stress to cucumber fruit yield and quality during summer. To investigate the potential metabolic mechanisms, this study employed untargeted metabolomics methods to analyze the effects of varying temperatures and carbon dioxide concentrations on the metabolomic profiles of cucumber fruits. Under high-temperature stress, elevated carbon dioxide concentrations altered 27 differential metabolites, including tyramine, xylitol, linolenic acid, L-asparagine, α-linolenic acid, and L-phenylalanine. These alterations are associated with the metabolic pathways of alanine, aspartate, glutamate, glutathione, glyoxylate, and dicarboxylic acids. Compared to the addition of carbon dioxide at normal temperatures, elevated carbon dioxide at high temperatures modified 38 differential metabolites, including vitamin B6, L-citrulline, inositol, L-aspartic acid, sucrose, and palmitic acid. These modifications were linked to the galactose metabolic pathway and the zeatin and arginine biosynthetic pathways. The accumulation of cysteine, glutamic acid, and glycine is essential for the formation of antioxidant glutathione; thus, cucumber fruits with higher amino acid content exhibit an enhanced capacity to withstand severe high-temperature stress. Under high-temperature conditions, elevated carbon dioxide adds complexity to the changes in differential metabolites within cucumber fruits. These fruits accumulate sugars, organic acids, and amino acids through the galactose metabolism pathway (map00052), the arginine biosynthesis pathway (map00220), and the glutamate synthesis pathway (map00250), thereby improving their heat resistance.