<p>Waterlogging is one of important abiotic stresses affecting crop production and food security globally. Sea barley (<i>Hordeum marinum</i>) is more waterlogging-tolerant than barley (<i>Hordeum vulgare</i> L.). To reveal the molecular mechanisms underlying the difference between two barley relatives (barley and sea barley), we analyzed their transcriptional and metabolic profiles in leaves under control and waterlogging conditions. Under waterlogging treatment, sea barley (accession H559) was less inhibited than barley (cultivar ZU9) in terms of relative fresh/dry shoot weight, chlorophyll and carotenoid content, and soluble/reducing sugar content, which was probably attributed to the up-regulation of the genes involved in photosynthesis in sea barley. Under waterlogging stress, a total of 1182 and 2348 differentially expressed genes (DEGs) were detected in sea barley and barley, respectively. There were some specific DEGs related to ROS detoxification identified in sea barley. On the other hand, a total of 94 and 92 differential metabolites were detected in sea barley and barley, respectively, and it showed that sea barley accumulated more sugars for energy supply under waterlogging stress. It may be assumed from the results that higher waterlogging tolerance in sea barley is attributed to stable photosynthesis, efficient ROS scavenging, more sugar accumulation and active TCA cycle, possibly regulated by <i>OEE2</i>, <i>ERF1</i>, and <i>SUS1</i> genes. These results provided fundamental adaptive strategies to decipher why sea barley had higher waterlogging tolerance than barley.</p>