This study elucidated storage carbon metabolism in a dynamic manner through kinetic model, metabolomics and stable metabolic flux analysis. Results revealed nutrient uptake rate, carbon availability and synthetic path rate accounted for the integration of process-compatible products. The uptake rate could be enhanced by promoting carbohydrate accumulation, inducing high performance of tricarboxylic acid cycle and anaplerotic routes. Values of specific rate for lipid from kinetic model and synthetic path rate from metabolic flux analysis revealed that conversion of carbon sinks occupied a key position in increasing productivities of lipid and astaxanthin to 302.34 and 1.83 mg g d, respectively. Additionally, economic estimation was applied to link cultivation factors with market scenario and demonstrated that regulating such carbon metabolism raised 30% increase of biomass value. This study therefore provided a new orientation to boost carbon efficiency that helped to engineer carbon flux from carbon source to targeted products precisely and rapidly.