Synechocystis sp. PCC 7338 (hereafter referred to as Synechocystis 7338) is a marine cyanobacterium that has the potential to produce photosynthetic pigments. In this study, we investigated the effects of various NaCl concentrations (0, 0.4, 0.8, and 1.2 M) on cell growth, photosynthetic pigments, and metabolites and intact lipid species profiles in Synechocystis 7338. The overall growth pattern of Synechocystis 7338 was similar under 0, 0.4, and 0.8 M NaCl conditions. Cell growth was retarded after reaching the exponential phase under 1.2 M NaCl; however, a similar growth pattern was observed after the exponential phase under 0.4 M NaCl (control group). The highest production of chlorophyll a (4.18 mg L-1), allophycocyanin (4.08 mg L-1), and phycoerythrin (1.70 mg L-1) were achieved under 1.2 M NaCl conditions. Altered metabolic and lipidomic profiles were observed at different NaCl conditions; significantly increased relative yields of glucosylglycerol, one diacylglyceryltrimethylhomoserine, one monogalactosyldiacylglycerol, and four phosphatidylglycerol species were observed under 1.2 M NaCl conditions using gas chromatography-mass spectrometry and direct infusion-mass spectrometry analyses. In addition, it was revealed that the photosynthetic activity recovered under 1.2 M NaCl conditions in long-term culture. Hydrogen peroxide content significantly increased under 1.2 M NaCl conditions. It is believed that glutathione content also significantly increased under high salinity conditions to retain the normal functioning of Synechocystis 7338. These results indicate that high salinity conditions for Synechocystis 7338 culture could be used for the large-scale production of chlorophyll a, allophycocyanin, phycoerythrin, and other bioactive metabolites.