Marine plankton communities are central to global biogeochemical cycles and climate regulation. Among them, mixotrophy, combining photosynthesis and phagotrophy, is increasingly recognized for its metabolic flexibility. However, the quantitative mechanisms governing resource acquisition and allocation in mixotrophs, and their responses to environmental change, remain poorly understood. Under global change, environmental factors such as light, temperature, and nutrient availability (e.g., nitrogen and phosphorus) strongly regulate metabolic allocation in mixotrophic phytoplankton, with important consequences for marine primary productivity and the carbon cycle. Current understanding is largely derived from freshwater or temperate systems and often relies on physiological observations or model extrapolations, while direct quantification of carbon and nitrogen fluxes under controlled conditions remains limited. Here, we use two marine mixotrophic, Ochromonas sp. and Florenciella sp., as model organisms. Under axenic conditions, we establish autotrophic and mixotrophic treatments and systematically manipulate light, nitrogen sources, and bacterial abundance. By integrating physiological assays, stable isotope tracing, and multi-omics analyses, we quantify carbon and nitrogen fluxes from photosynthesis and phagotrophy. Combining physiological and molecular perspectives, this study provides a quantitative framework for understanding how environmental conditions regulate nutritional strategies and resource allocation in marine mixotrophs across distinct taxonomic groups.