Carbon quantum dots (CQDs) were synthesized by hydrothermal synthesis of a symbiotic microalgal community consisting of three species. Two distinct fluorescent CQDs, emitting yellow and green light, were separated through dialysis. The morphology and fluorescent properties were tested. To evaluate their environmental impact, microalgae-derived and commercial CQDs were introduced as pollutants and tested on microalgal cells under red, green, and white light conditions. Inhibition rate, reactive oxygen species signals and intracellular biomolecule synthesis (proteins, carbohydrates, and lipids) were systematically analyzed. The results demonstrated that microalgae-derived CQDs have a spherical structure and are capable of emitting light at 431nm and 479nm and induced less cellular damage than commercial CQDs. Furthermore, CQDs exhibited distinct regulatory effects on biomolecule synthesis under different light conditions: all CQDs inhibited protein synthesis, commercial red-emitting commercial CQDs enhanced carbohydrate accumulation, and microalgae-derived CQDs promoted lipid production. This study highlights the toxicity of CQDs on microalgae and their influence on intracellular component synthesis, providing foundational insights for optimizing microalgae-based biotechnological applications.