Pressurized CEC (pCEC) coupled with ESI-QTOF-MS using a sheathless interface was applied for metabolomics to develop an alternative analytical method for metabolic profiling of complex biofluid samples such as urine. The hyphenated system was investigated with mixed standards and pooled urine samples to evaluate its precision, repeatability, linearity, sensitivity, and selectivity. The applied voltage, mobile phase, and gradient elution were optimized and applied for the analysis of urinary metabolites. Multivariate data analysis was subsequently performed and used to distinguish lung cancer patients from healthy controls successfully. High separation efficiency has been achieved in pCEC due to the EOF. For metabolite identification, the pCEC-MS separation mechnism was helpful for discriminating the fragment ions of glutamine conjugates from co-eluted metabolites. Three glutamine conjugates, including phenylacetylglutamine, acylglutamine C8:1, and acylglutamine C6:1 were identified among 16 differential urinary metabolites of lung cancer. Receiver-operating-characteristic analysis of acylglutamine C8:1 resulted in an area-under-curve value of 0.882. Overall, this work suggests that this pCEC-ESI-QTOF-MS method may provide a novel and useful platform for metabolomic studies due to its superior separation and identification.