To explore the adaptive mechanism of Cynodon dactylon under flooding, Cynodon dactylon plants with similar growth were divided into a non-flooded control group (A1) and a treatment group (A2). The latter consisted of a submersion depth of 30 cm. After submergence of A2 for fifteen days, sampling of the two groups was carried out simultaneously. Thereafter, the total RNA of the samples was extracted for transcriptome sequencing. The de novo sequencing data of A1 and A2 revealed 128031 and 83363 high-quality unigenes, respectively. 28844 differentially expressed genes (DEGs) were found between A1 and A2, of which 11858 DEGs were up-regulated and 16986 were down-regulated. Functional annotation showed that these DEGs were mainly concentrated in the transcription, translation, carbohydrate metabolism, and environmental adaptation. The results of signal pathway enrichment showed that 103 signaling pathways, including plant defense responses against pathogens, metabolism, photosynthesis, individual fitness development, and antioxidant activity, were related to the adaptability of Cynodon dactylon to flooding. DEGs were randomly selected for real-time quantitative reverse transcription PCR (qRT-PCR), and the results of quantitative analysis of fluorescence were the same as that of sequencing, which indicated that the expression of DEGs was more reliable. It might provide a basis for further excavation of regulatory genes and functional genes, which are associated with the adaptability of Cynodon dactylon in flooding.