BackgroundAs damage to the ecological environment continues to increase amid unreasonable amounts of irrigation, soil salinization has become a major challenge to agricultural development. Melatonin (MT) is a pleiotropic signal molecule and indole hormone, which alleviates the damage of abiotic stress to plants. MT has been confirmed to eliminate reactive oxygen species (ROS) by improving the antioxidant system and reducing oxidative damage under adversity. However, the mechanism by which exogenous MT mediates salt tolerance by regulating the photosynthetic capacity and ion balance of cotton seedlings still remains unknown. In this study, the regulatory effects of MT on the photosynthetic system, osmotic modulators, chloroplast, and anatomical structure of cotton seedlings were determined under 0–500 μM MT treatments with salt stress induced by treatment with 150 mM NaCl.ResultsSalt stress reduces the chlorophyll content, net photosynthetic rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, PSII photochemical efficiency, PSII actual photochemical quantum yield, the apparent electron transfer efficiency, stomata opening, and biomass. In addition, it increases non-photochemical quenching. All of these responses were effectively alleviated by exogenous treatment with MT. Exogenous MT reduces oxidative damage and lipid peroxidation by reducing salt-induced ROS and protects the plasma membrane from oxidative toxicity. MT also reduces the osmotic pressure by reducing the salt-induced accumulation of Na+ and increasing the contents of K+ and proline. Exogenous MT can facilitate stomatal opening and protect the integrity of cotton chloroplast grana lamella structure and mitochondria under salt stress, protect the photosynthetic system of plants, and improve their biomass. An anatomical analysis of leaves and stems showed that MT can improve xylem and phloem and other properties and aides in the transportation of water, inorganic salts, and organic substances. Therefore, the application of MT attenuates salt-induced stress damage to plants. Treatment with exogenous MT positively increased the salt tolerance of cotton seedlings by improving their photosynthetic capacity, stomatal characteristics, ion balance, osmotic substance biosynthetic pathways, and chloroplast and anatomical structures (xylem vessels and phloem vessels).ConclusionsOur study attributes help to protect the structural stability of photosynthetic organs and increase the amount of material accumulation, thereby reducing salt-induced secondary stress. The mechanisms of MT-induced plant tolerance to salt stress provide a theoretical basis for the use of MT to alleviate salt stress caused by unreasonable irrigation, fertilization, and climate change.