Substituting agricultural by-products for glucose as a carbon source is an effective strategy for reducing the cultivation cost of Chlorella sp. However, the response mechanism of Chlorella sp. to variations in carbon sources remains unclear, and the potential of microalgal biomass for food development warrants further exploration. This study used hydrolysate of sweet sorghum stem juice (HSJ) for the mixotrophic cultivation of Chlorella sp. And transcriptomic analysis was performed to investigate the physiological and metabolic mechanisms as well as the biosynthesis of value-added compounds (e.g., pigments and proteins) of Chlorella sp. in response to changes in carbon sources. The HSJ + NM group (HSJ supplemented with nitrogen and minerals) significantly increased total chlorophyll, carotenoids, lutein, and protein levels by 18.02 %, 13.34 %, 35.95 %, and 20.36 %, respectively, compared to the control (adjusted BG-11 medium supplemented with 10 g/L glucose). Notably, transcript levels of genes for multiple key enzymes involved in glycolysis/gluconeogenesis, TCA cycle, oxidative phosphorylation pathway, and photosynthesis pathways were significantly up-regulated. The activity of these pathways promoted the pigments and proteins synthesis in Chlorella sp. Encouragingly, the cost of cultivating Chlorella sp. with HSJ + NM (0.495 USD/kg) was 43.35 % of glucose (1.142 USD/kg). Further, by fermenting Chlorella sp. cultures with Saccharomyces cerevisiae and further homogenizing and blending the fermentation broth, we developed a nutritious and palatable Chlorella sp. fermented beverage, addressing the common issue of algal odor in such products. This study provides theoretical and practical foundations for the mixotrophic cultivation of microalgae and the application of microalgal biomass in food innovation.