To promote biomass and lipid productivity of microalgae in a continuous two-stage cultivation process with 15% CO2, adequate phosphorus was supplemented in the second stage of cultivation involving nitrogen starvation and stored with regulated existence patterns to improve the metabolic activity of Chlorella PY-ZU1. The results showed that the applied strategy allowed microalgae biomass concentration and lipid productivity 1.3 and 2.2 times higher, respectively, than those without phosphorus supplementation. Chlorella PY-ZU1 cells cultivated with an adequate amount of phosphorus were analyzed by electron microscopy that revealed the distribution of polyphosphates in the cytoplasm, vacuoles, and along the cell membranes. P-31 nuclear magnetic resonance (31P NMR) showed polyphosphate, pyrophosphate, and orthophosphate contents of 0.59, 2.46, and 8.21 mg g−1, respectively, in the extracts of Chlorella PY-ZU1 cells obtained by the NaOH-EDTA method. Moreover, the ATP synthase involved in the photosynthesis and oxidative phosphorylation pathways was up-regulated to promote biomass productivity, while the enzymes involved in carbon fixation and glycerolipid metabolism were up-regulated to facilitate lipid accumulation in cells.