Abstract: Chlorella sorokiniana (Chlorophyta) is a ubiquitous, fast-growing green alga that can grow under heterotrophic conditions to produce biomass and lipids. However, the low protein content of C. sorokiniana cells grown under heterotrophic conditions limits their commercial applications. This study revealed that the protein contents of the C. sorokiniana GT-1 cells increased significantly when these cells were transferred to the photoautotrophic from the heterotrophic conditions. Transcriptomics analysis showed that the glycolysis and pentose phosphate pathways were significantly upregulated and those genes encoding key enzymes involved in the nitrogen transport and assimilation were significantly induced. As for the biosynthesis of amino acids (aa), only those involved in the glutamic and pyruvate families were upregulated. In addition, many genes encoding photosynthetic proteins were expressed under heterotrophic conditions, and most of them were up-regulated during 24 hours after transiting from heterotrophic conditions to photoautotrophic conditions. These results indicated that the enhanced protein content of C. sorokiniana GT-1 cells transiting from the heterotrophic to photoautotrophic conditions may be attributable to the elevated absorption and utilization of nitrate, production of reducing equivalents, biosynthesis of some amino acids, and regeneration of photosynthetic proteins. This study provides new insights into enhancing the protein production of C. sorokiniana GT-1 by optimizing culture conditions or metabolic engineering.