Nitrogen starvation has been an effective method to enhance the lipid content in microalgae, but low biomass means the method is far from large-scale application. In this study a combination of phytohormones, indolebutyric acid (IBA) and naphthylacetic acid (NAA), was used to verify whether phytohormones can assist two microalgae, Scenedesmus SDEC-8 and Chlorella sorokiniana SDEC-18, to resist nitrogen depletion, and achieve satisfactory biomass and lipid productivity. The two algae grew poorly but accumulated high lipid concentrations under nitrogen-depleted condition without phytohormones. However, phytohormone addition maintained the biomass concentration, and furthermore yielded lipid productivities (SDEC-8: 26.7 mg/L/d, SDEC-18: 25.9 mg/L/d) almost 3 times as high as those in BG11. The oxidative damage caused by nitrogen depletion could be alleviated by phytohormones. The investigation demonstrated that phytohormone supplementation simultaneously improved lipid accumulation and maintained growth of microalgae, while also optimizing the biodiesel properties compared with the tactic of nitrogen depletion alone.