C-Phycocyanin is a high-value bioproduct synthesized from cyanobacterium Arthrospira platensis. To facilitate its application, advanced dynamic models were built to simulate the complex effects of light intensity, light attenuation, and nitrate concentration on cell growth and pigment production. When these models were compared to the experimental results, their accuracy was verified in both batch and fed-batch processes. Three key findings are presented in this work. First, a noticeable difference between the optimal light intensity for cell growth (282 μmol m–2 s–1) and phycocyanin synthesis (137 μmol m–2 s–1) is identified. Second, light attenuation is demonstrated to be the primary factor causing the decrease of intracellular phycocyanin content instead of nitrate concentration in the fed-batch process, whereas it has no significant effect on total phycocyanin production. Finally, although high nitrate concentration can enhance cell growth, it is demonstrated to suppress intracellular phycocyanin accumulation in long-term operation.