•Overexpression of sly-miR398b increased the sensitivity to salinity in tomato.•Overexpression of sly-miR398b enhanced the oxidative stress via the accumulation of O2− other than H2O2.•sly-miR398b promoted the accumulation of O2− via inhibition of CSD1 expression.•sly-miR398b regulated the expressions of antioxidant genes, activity of antioxidant enzymes and contents of antioxidants.•Overexpression of sly-miR398b induced photoinhibition and inhibited the photosynthesis under salinity. microRNA398 (miR398) is known to be involved in response to abiotic stress in some plant species through transcriptionally regulating its targets, Cu/Zn superoxide dismutase (CSD). However, the role of miR398 has not yet been characterized in horticultural plants. It also remains unclear as how miR398 regulate antioxidant system and photosynthesis under salinity. To address this issue, we generated transgenic tomato lines overexpressing its own miR398 and exposed them to salt stress. Overexpression of sly-miR398b inhibited the plant growth under salinity, including less shoot and root biomass and shorter plant height. In addition, the transgenic plants accumulated more O2− under normal and saline conditions, and consequently suffered from more severe oxidative damage. Further analyses revealed that overexpression of sly-miR398b downregulated the expression of CSD, APX and CAT, leading to the reduced activities of SOD, APX and CAT, and the contents of reduced glutathione. In addition, the transgenic plants exhibited lower rates of photosynthesis and higher photoinhibition under salinity in comparison with the wild type plants. The data provide new evidence on the miR398 mediated ROS metabolism network underlying salt stress response in tomato.