Arbuscular mycorrhiza can improve the salt-tolerance of host plant. A systematic study of mycorrhizal plant responses to salt stress may provide insights into the acquired salt tolerance. Here, the transcriptional profiles of mycorrhizal Sesbania cannabina shoot and root under saline stress were obtained by RNA-Seq. Using weighted gene coexpression network analysis and pairwise comparisons, we identified coexpressed modules, networks and hub genes in mycorrhizal S. cannabina in response to salt stress. In total, 10,371 DEGs were parsed into five coexpression gene modules. One module was positively correlated with both salt treatment and arbuscular mycorrhizal (AM) inoculation, and associated with photosynthesis and ROS scavenging in both enzymatic and nonenzymatic pathways. The hub genes in the module were mostly transcription factors including WRKY, MYB, ETHYLENE RESPONSE FACTOR, and TCP members involved in the circadian clock and might represent central regulatory components of acquired salinity tolerance in AM S. cannabina. The expression patterns of 12 genes involved in photosynthesis, oxidation-reduction processes, and several transcription factors revealed by qRT-PCR confirmed the RNA-Seq data. This large-scale assessment of Sesbania genomic resources will help in exploring the molecular mechanisms underlying plant-AM fungi interaction in salt stress responses.