Lipid-extracted algae (LEA) can be processed via acetone, butanol and ethanol fermentation to produce butanol as an additive to algal biofuel, but direct fermentation was ineffective. In this study, nitrogen and phosphorus regulation for algae cultivation was applied to modify the biochemical composition of algal biomass and hence improve butanol production from LEA. The results show that when nitrogen starvation and excess phosphorus were used during algae cultivation, a significant rise of starch productivity and decline of protein productivity for algal biomass were obtained, which resulted in the highest butanol productivity of 20.16 mg L−1 d−1, a 5.48-fold increase over traditional one-stage cultivation. Mechanism analysis suggested that nitrogen starvation enhanced lipid and starch contents and reduced protein content, which modified C/N ratio of LEA, prevented acid crash and improved butanol production; excess phosphorus modified amino acid contents of phenylalanine and arginine, which strengthened fluxes directing to butanol generation. Through this investigation, the approach of using nitrogen starvation and excess phosphorus to modify biochemical composition of algal biomass and subsequently improve butanol production of LEA was demonstrated to be applicable.