This study aims to explore the protein phosphorylation regulatory mechanism of the microalgae Chromochloris zofingiensis in response to carbon source variation and mTOR pathway inhibition. A total of four experimental groups were set up, including control group, glucose treatment group, 2-deoxy-D-glucose treatment group, and AZD-8055 treatment group, with three biological replicates for each group. Quantitative phosphoproteomics analysis was performed using mass spectrometry platform supported by Majorbio Bio-pharm Technology. This dataset contains all raw phosphoproteomic data for identifying differentially phosphorylated proteins and key regulatory phosphorylation sites involved in metabolic and signal transduction pathways.