Amid global food shortage, alternative cost-effective protein sources are urgently needed for aquaculture and animal feed. Without a rigid cell wall, Euglena gracilis provides extractable, digestible proteins, and its high productivity makes it an ideal feed source. This study investigates the effects of different inorganic nitrogen sources on the biomass and biochemical composition of E. gracilis, and discusses the mechanisms of its nutrient transformation via proteomics. Results show ammonium nitrogen optimizes growth and protein accumulation by serving as an energy-efficient precursor for biomolecule synthesis compared to nitrate. Additionally, sulfate supplies sulfur for amino acid synthesis, and ammonium sulfate further enhances protein production. Under high-protein conditions, lipids and pigments increase while paramylon decreases significantly, underscoring nitrogen's role in carbon allocation and energy metabolism. This study establishes a metabolic framework for nitrogen-sulfur coordinated regulation of protein synthesis in E. gracilis, paving the way for its industrial application as a next-generation protein resource.