This study was aimed to investigate how exogenous manganese (Mn) would limit damage in the oxygen-evolving complex (OEC) and photosynthetic apparatus of maize seedlings caused during seawater vulnerability. In this study, seawater was applied in 2-week-old maize (Zea mays L.) seedling, and the degree of damage of photosynthetic pigment pool, the OEC, and net electron transport rate were observed. Mn supplement was also added in maize seedlings to limit the damage of the OEC and photosynthetic apparatus caused during salinity. Leaf relative water content (RWC), fresh weight (FW), and photosynthetic pigment pool (chlorophyll a, chlorophyll b, and carotenoids) sharply declined after 7 days of treatment; however, Mn supplement increased these values. Chlorophyll fluorescence induction (OJIP) transients showed low Fv/Fo, an additional K step, enhanced variable fluorescence (VK) and degree of damage to the OEC (WK) during salinity, and indicates damage of OEC at electron donor side of photosystem II (PSII). The OEC intact within PSII was a primary damage center during salinity which inhibited electron transport process that resulted in a huge loss of maximum quantum yield of PSII (Fv/Fm), but a significant recovery in photosynthetic apparatus was observed after exogenous application of manganese. Structural and functional integrity of the photosynthetic apparatus was recovered up to a certain extent after exogenous application of Mn. Findings from this study should help to understand the basic knowledge of photosynthetic apparatus efficiency in response to damage caused by exposure to seawater. Outcomes of this study will be used to mitigate salinity problem with Mn supplement for growth and development of crops.