In this study, temporal variations of microalgae growth and lipid accumulation in response to different nitrogen concentrations in media were investigated and discussed in detail, using a mutant Chlorella vulgaris SDEC-3M as a model. The results show that a short-term of dramatic lipid accumulation and nonsignificant descent of biomass productivities can be concomitant in SDEC-3M during early N-deficient stage (buffer period). It was found that the maximum lipid productivities of 63.52 mg L-1 d(-1) occurred after 24 h N-shift. It means that, obtained lipid productivity under two-stage strategy with 24 h N-deficient stage was approximately three times as high as the maximum one obtained under N-rich condition and the final one obtained during longer N-deficient culture. Batch culture mode, higher light intensity and light/dark cycle in cooperation with N-rich/N-deficient cycle were also suggested as feasible scheme to improve lipid productivity in large scale culture. Additionally, the fatty acid profiles analysis indirectly showed that the properties of biodiesel from SDEC-3M majorly satisfied biodiesel standards. The fuel performances varied with N-deficient culture time, meaning that better combustion performance, oxidation stability, and exhaust emissions level related to longer N-deficient stage, while the biodiesel produced form N-deficient would perform well under low temperature. The results mean that SDEC-3M-derived biodiesels with customized process designs have commercial potential in the aspects of productivity and quality. (C) 2016 Elsevier Ltd. All rights reserved.