The salt-tolerant microalgae are extremely few and salt-tolerance mechanism is unclear, requiring urgent exploration of salt-tolerance mechanism of known microalgae. This study was first to reveal the salt-tolerance mechanism of Golenkinia sp. SDEC-16 by investigating the growth and metabolism under different salinities and high salinity long-term cultivation. SDEC-16 can survive under high salinity and resume normal growth after NaCl removal. Under long-term stress, SDEC-16 had higher lipid content and productivity than BG11. However, the suppressed Fv/Fm (58.4%) and Fv/F0 (84.0%) along with the increased reactive oxygen species (×6.6), and superoxide dismutase (×1.7) during the treatment revealed NaCl-induced photosynthetic inhibition and oxidative stress. RNA sequencing results showed inhibition of the photosynthetic system, and the enhancement of pathways such as nitrogen metabolism, energy metabolism, and lipid synthesis contributed to the good function of chloroplast, energy supply, and metabolic activity of SDEC-16. This study provides theoretical support for large-scale microalgal cultivation in seawater.