Mepiquat chloride (MC) priming alleviates the effects of salt stress during seed germination in cotton (Gossypium hirsutum L.), but the mechanisms underlying its effects are unknown. We found that MC priming increases salt tolerance, as evidenced by marked increases in seed vigor and germination rates, and alleviated salt toxicity by reducing Cl?accumulation in germinating seeds. Consistently, electrophysiological experiments revealed that the seeds with MC priming displayed superior Cl? exclusion ability in the root apex. These beneficial effects of MC priming were abolished by the abscisic acid (ABA)-synthesis blocker fluridone under salt stress. MC priming induced an early response to acclimatization and stress, as indicated by rapidly increasing ABA content during initial exposure to salt stress. Transcriptome analyses revealed that MC priming induced an array of differentially expressed genes (DEGs) in germinating seeds. The most noticeable changes in germinating seeds were MC priming-induced increases in the expression of DEGs encoding components of ABA biosynthesis, ABA catabolism, and ABA signaling pathways under salt stress. MC priming also increased the expression of some DEGs encoding Cl?ion transporters (e.g. CCC, SLAC1/SLAH1/SLAH3, CLC, and ALMT9) in germinating seeds. These results indicate that MC priming-induced ABA contributes to Cl? homeostasis in tissues and acts as a positive regulator of salt tolerance via regulation of Cl? transporters (particularly CCC and SLAC1/SLAH1/SLAH3). Taken together, these findings shed light on the molecular mechanism underlying MC-mediated tolerance to salt stress during seed germination.