Fucoxanthin and fatty acids are active substances that are beneficial to the growth and immunity of humans and aquatic animals. However, relatively few species have been exploited for fucoxanthin and fatty acids in the industry. At the same time, due to its low extract content, poor stability, high production cost, and serious seasonal and regional limitations, the industry cannot normally meet the greater demand of the international market. Therefore, this experiment seeks to improve the fucoxanthin and fatty acid content of C. weissflogii by adjusting the nitrogen concentration in the culture medium. It was found that when the nitrogen concentration was 150 mg L−1, the cell number was 1.5 × 106 cell mL−1, and the average biomass was 0.75 g L−1. The mean value of carotenoid concentration was 2.179 mg L−1. The average concentration of fucoxanthin was 1.547 mg g−1. When the nitrogen concentration was 75 mg L−1, the fatty acid content reached its highest. By adjusting the concentration of nitrogen, the contents of fucoxanthin and fatty acids were increased. The results provided a theoretical basis for commercial extraction of fucoxanthin and fatty acids and further promoted the industrialization of fucoxanthin and fatty acids.