Sweet sorghum is an annual C4 crop that has high salt tolerance. However, the role of hormones in salt tolerance of sweet sorghum remains unelucidated. In the present study, growth parameters, endogenous hormone concentrations, and transcriptomes of leaves and roots of two inbred lines of sweet sorghum (salt-tolerant M-81E and salt-sensitive Roma) were analyzed under 0 or 150 mM NaCl in order to elucidate hormonal regulation for salt tolerance in sweet sorghum. We found that salt stress inhibited the growth of both genotypes. The concentration of abscisic acid (ABA) changed more significantly in M-81E leaves, and concentration of jasmonate (JA) changed more significantly in Roma roots. While, the concentration of indole-3-acetic acid (IAA) increased in both genotypes, particularly in the leaves. We identified 17 and 15 differentially expressed genes in M-81E between control plants and those subjected to salt stress annotated into pathways of hormone biosynthesis and hormone signal transduction, respectively. In Roma, 16 and 34 differentially expressed genes annotated into pathways of hormone biosynthesis and hormone signal transduction were identified, respectively. Hormone biosynthesis, and signal transduction, may play an important role in regulating the growth and development of sweet sorghum under salt stress. In salt-tolerant inbred line M-81E, ABA may play a key role in salt stress response. In salt-sensitive inbred line Roma, JA may act as the key hormone in response to salt stress. These revealed that hormones are involved in the response of sweet sorghum to salt stress. Furthermore, in different inbred lines, different hormones might play significant roles in regulating the growth and development of sweet sorghum through different regulation pathways.