A life-cycle analysis (LCA) of greenhouse gas (GHG) emissions and energy use was performed to study bio-jet fuel (BJF) production from micro-algae grown in open ponds under Chinese conditions using the Tsinghua University LCA Model (TLCAM). Attention was paid to energy recovery through biogas production and cogeneration of heat and power (CHP) from the residual biomass after oil extraction, including fugitive methane (CH4) emissions during the production of biogas and nitrous oxide (N2O) emissions during the use of digestate (solid residue from anaerobic digestion) as agricultural fertilizer. Analyses were performed based on examination of process parameters, mass balance conditions, material requirement, energy consumptions and the realities of energy supply and transport in China (i.e., electricity generation and heat supply primarily based on coal, multiple transport modes). Our LCA result of the BJF pathway showed that, compared with the traditional petrochemical pathway, this new pathway will increase the overall fossil energy use and carbon emission by 39% and 70%, respectively, while decrease petroleum consumption by about 84%, based on the same units of energy service. Moreover, the energy conservation and emission reduction benefit of this new pathway may be accomplished by two sets of approaches: wider adoption of low-carbon process fuels and optimization of algae cultivation and harvest, and oil extraction processes.