Urolithiasis is a common urological disease with a high morbidity and recurrence rate, of which calcium oxalate (CaOx) is the most common type of stone that underlies the disease. However, the potential metabolic mechanisms of CaOx urolithiasis remain unclear. The present study aimed to seek potential biomarkers and metabolic mechanisms of CaOx urolithiasis in adults. Urine samples were collected from 36 healthy individuals and 36 patients diagnosed with bilateral upper-urinary-tract stones. All of the stones were composed of CaOx. Ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to perform a metabolic fingerprinting analysis. Principal component analysis (PCA) and orthogonal partial least-squares determinant analysis (OPLS-DA) were carried out to analyze the multivariate data. There were 18 differential metabolites identified, which mainly involved caffeine, phenylalanine, galactose, and tyrosine metabolism. The results revealed potential urinary biomarkers, via metabolic fingerprinting of adults with CaOx urolithiasis, which may help to improve future metabolic evaluation of urolithiasis. The elucidated metabolic pathways may have potential applications as novel treatment targets of CaOx urolithiasis. Additionally, our study suggests that the UPLC-Q-TOF/MS platform may offer new insights into the pathobiology of urolithiasis.