To improve lipid and astaxanthin productivity without compromising biomass during the whole cultivation period, carbon-dependent kinetics involving nitrogen stress was applied under excess light to elevate intracellular carbon availability and metabolic activity of Chromochloris zofingiensis. Results suggested that fed-batch strategy proposed could increase lipid and astaxanthin productivity to 457.1 and 2.0 mg L−1 d−1, respectively. Biomass productivity at 1084.3 mg L−1 d−1 was comparable with that under suitable condition. Then 13C tracer-based metabolic flux analysis (13C-MFA) demonstrated that central carbon metabolism provided ATP, NADPH and carbon availability for lipid biosynthesis during the strategy. In combination with targeted metabolite analysis, 13C-MFA revealed that the strategy improved precursor content for lipid biosynthesis and elevated path rate to synthesize C16:0 and C18:0. The enhanced lipid content potentially accounted for the high biomass productivity. Therefore, comprehensively understanding relationships between carbon availability and carbon conversion could precisely design strategy for productivity improvements during cultivation.