Heat stress (HS) is a main environmental challenge affecting the animal welfare and production efficiency in pig industry. In recent years, numerous reports have studied the alterations in gene expressions and protein profiles in heat-stressed pigs. However, the use of metabolome to unravel adaptive mechanisms of finishing pig in response to chronic HS have not yet been elucidated. We aimed to investigate the effects of chronic HS on serum metabolome in finishing pigs, and to identify the biomarkers of heat stress. Pigs (n = 8 per treatment) were exposed to either thermal neutral (TN; 22 °C) or heat stress (HS, 30 °C) conditions for three weeks. Serum metabonomics of TN- and HS-treated pigs were compared using the GC-MS approach. Metabonomics analysis revealed that twenty-four metabolites had significantly different levels in TN compared to HS (variable importance in the projection values >1 and p < 0.05). These metabolites are involved in carbohydrate, amino acid, fatty acid, amines metabolism, and gut microbiome-derived metabolism. Three serum monoses (glucose, mannose 2, and galactose) and 6-phosphogluconic acid were decreased, indicating insufficient source of fuel for energy supply, resulting in negative energy balance (NEB) in heat-stressed pigs. Increased levels of non-esterified fatty acid (myristic acid, palmitic acid, and linoleic acid) and short-chain fatty acids (3-hydroxybutanoic acid and maleic acid) suggested fat decomposition compensating for energy shortage, which was an adaptive response to NEB. Increased concentrations of fluorine, lyxose 1, and D-galacturonic acid were significantly correlated with the levels of acute phase proteins (HP, LBP, α2-HSG, and Lysozyme), suggesting acute phase response in HS-stressed pigs. These metabolites are expected to be novel biomarkers of chronic HS in pigs, yet the use of which awaits further validation.