Melatonin (MT) can protect plants against abiotic stress. In order to explore whether melatonin can improve photosynthetic function under NaCl stress, Solanum lycopersicum L. cv. Liaoyuanduoli were exposed to 150 mmol L−1 NaCl stress with or without pretreatment with 150 μmol L−1 melatonin. The results showed that NaCl stress can lead to reduced chlorophyll content, lower photosynthetic function, increased reaction oxygen species (ROS) levels, and decreased PSII activity. These changes were mainly due to the reduction in oxygen-evolving complex (OEC) activity on the donor side of PSII and the blockage of electron transfer from QA to QB on receptor side of PSII. The donor side of PSII was more sensitive to NaCl stress relative to the receptor side of PSII. Interestingly, application of MT enhanced tomato NaCl tolerance. MT reduced the production of ROS by balancing the distribution of photosynthetic electron flux, facilitated the repair of PSII by maintaining the abundance of Psb O and D1, and promoting the ability of the donor and acceptor sides of PSII to deliver electrons. MT also enhanced the scavenging ability of ROS by stimulating the activity of enzymes involved in the AsA-GSH cycle.