Field and Greenhouse studies that attempted to describe the molecular responses of trees under waterlogging (WL) combined with salinity (ST) are quasi-inexistent. To dissect plant-specific molecular responses and patterns under SWL, we integrated transcriptional and metabolic analyses involving common differentially expressed genes (DEGs) and metabolites (DMs) patterns in Dalbergia odorifera leaflets. SWL-treated seedlings exhibited an impressively high number of DEGs and DMs compared to ST or WL. Although the main common DEGs and DMs showed a neutral pattern, gene ontology enrichment following the classification in different functional categories of SWL-transcripts displayed a predominant synergistic pattern mode. Hierarchical and silhouette analysis regrouped different morpho-physiological clusters following the treatment, SWL was mainly grouped with both single stress. SWL induced a massive shutdown of the photosynthesis apparatus through LHCBs- and PSA-related genes. Starch and plastoglobuli synthesis appeared to be drastically affected by SWL, while ABA content confirmed by ABA synthesis-related genes (ABF, ABA1, and NCED) variations showed a less-needed role. NXN (Nucleoredoxin) genes are the main factors that sustain the antioxidant system under SWL. Here we provide the first molecular responses, characterization, and patterns of a tree under SWL that would significantly shed light on our understanding of the molecular mechanisms underlying combined stress.