<p><i>Cyclotella cryptica</i>, a model diatom known for its robust adaptability to variable salinity and temperature conditions, is a promising candidate for large-scale biotechnological applications. Nutrient availability, particularly nitrogen and phosphorus, plays a crucial role in the metabolic activities of microalgae, influencing its industrial utility. Exploring the relationship between these essential nutrients and both the yield and biochemical composition of this microalga is crucial for optimizing cultivation strategies. However, research focusing on the effects of nitrogen and phosphorus on <i>C. cryptica</i> remains limited. We investigated the impacts of varying concentrations of nitrate (0.25–3.96 mmol/L) and phosphate (14.4–229.6 µmol/L) on <i>C. cryptica</i> culture by analyzing its growth performance, photosynthetic activity, biochemical composition, and biosilica deposition. Results indicate that <i>C. cryptica</i> exhibited enhanced growth, photosynthetic efficiency, and carotenoid production under higher nutrient concentrations. However, the effects of nitrate on macronutrients composition and fatty acids profile differed from those of phosphate. Specifically, increased nitrate levels resulted in higher concentrations of polyunsaturated fatty acids (PUFAs) at the expense of saturated fatty acids (SFAs), while increased phosphate levels were associated with increased PUFAs and reduced monounsaturated fatty acids (MUFAs). Additionally, biosilica deposition was weakened by elevated nitrate but enhanced by increased phosphate levels. This study improved our understanding of nutrient-mediated regulatory mechanisms in diatoms and contributed valuable data to the broader field of algal biotechnology. Moreover, these findings are expected to advance the development of tailored nutrient management strategies, thereby enhancing the industrial potential of <i>C. cryptica</i>.</p>