Microalgae produced lipids, pigments, lutein, and valuable chemicals under stressful conditions, making them as attractive feedstock for biorefineries. However, high cell density culture of microalgae in harsh condition using seawater is still a challenge. In this study, we used aminobutyric acid (GABA) from an in vitro biotransformation of monosodium glutamate (MSG) to alleviate salinity stress in Chlorella sorokiniana (Cs). Initially, Chlorophyll a/b content was suppressed under the stress of 20 g/L sodium chloride (NaCl), leading to an extreme decline in protein and pigment accumulation. While the biomass and protein of Cs cultured in 10 g/L NaCl reached 3.44 g/L and 1.14 g/L with 5 mM GABA, with 56.3% and 171% increase compared to control. The optimal conditions were 10 mM GABA and 20 g/L NaCl in modified BG11 medium, with a biomass, protein, lutein and β-carotene content of 4.56 g/L, 2.07 g/L, 24 mg/L and 27.48 mg/L, respectively. Finally, protein from Cs was used as a prebiotic for cultivating Escherichia coli Nissle 1917 (EcN) and Lactobacillus rhamnosus ZY (LGG). We provided an effective and sustainable approach for the simultaneous production of biomass and high-end products by microalgae using GABA and seawater for the first time.