Illumination of the molecular mechanisms involved in the pathogenesis of coronavirus disease 2019 (COVID-19) helped to discover therapeutic targets. To determine the metabolomic profile of circulating plasma from COVID-19 recovered with pulmonary sequelae 3 months after discharge, a random, outcome-stratified case-control sample was studied. Enrollment of 103 recovered COVID-19 patients and 27 healthy donors were taken, and pulmonary function tests were performed, computerized tomography (CT) scans, laboratory examinations, and liquid chromatography-mass spectrometry. Plasma metabolite profiles of COVID-19 recoveries with abnormal pulmonary function differed from those of healthy donors or subjects with normal pulmonary function. The alterations were found to be associated with disease severity and mainly involved amino acid and glycerophospholipid metabolic pathways. Moreover, increased levels of triacylglycerols, phosphatidylcholines, prostaglandin E2, arginine, and decreased levels of betain and adenosine were found to be associated with pulmonary carbon monoxide diffusing capacity and total lung capacity. In addition, the global plasma metabolomic profile differed between subjects with abnormal and normal pulmonary function. Further, a metabolite-based examination was thought to help identify the mechanisms underlying pulmonary dysfunction in COVID-19 survivors and provide potential therapeutic targets in the future.