Cognitive impairment commonly accompanies clinical syndromes associated with stroke. The identification of laboratory markers of post-stroke cognitive impairment (PSCI) may help detect patients at increased risk of cognitive deterioration and determine the appropriate treatment regimes. A non-targeted metabolomics approach based on ultra-high performance liquid chromatography coupled with Q-TOF mass spectrometry was applied to study PSCI. The stroke patients were significantly distinguishable from the healthy subjects. Stroke patients could be well-stratified based on cognitive impairment. Several differential serum metabolites were further identified for post-stroke non-cognitive impairment (PSNCI) and PSCI patients, suggesting metabolic dysfunction in inflammation, neurotoxicity, bioenergetic homeostasis, oxidative stress, and apoptosis. In total, three serum metabolites (glutamine, kynurenine, and LysoPC(18:2)) were identified as candidate diagnostic biomarkers for PSCI, and their combined use yielded good diagnostic capacity for PSCI by receiver operating characteristic curves. The present metabolomics study provided a novel strategy for stratifying stroke patients with cognitive impairment using serum-based metabolite markers, which could be of great importance in understanding the pathological mechanisms and determining the appropriate treatment regimes of PSCI patients.