A microalgae-based energy system, which is a combination of different microalgae-to-biodiesel chains and an integrated cogasification combined cycle (ICGCC) system, is presented. To address the low environmental impacts, the electricity is generated from ICGCC to meet the load demand from the microalgae-to-biodiesel chains and the flue gas exits from ICGCC to meet the demand of growing algal culture. To achieve the microalgae-based energy system with minimum life cycle greenhouse gas (GHG) emissions, the first step is to develop the superstructure model based on GAMS, the second step is to use the optimal heat exchanger network to maximize the heat recovery of ICGCC, and the third step is to find the optimal combination of the microalgae-to-biodiesel chain and optimal operating conditions of ICGCC by solving the global optimization of nonconvex mixed-integer nonlinear programming (MINLP) problem. For the scope of well-to-tank (WIT), the optimal microalgae-based energy system reduces 16.80% greenhouse gas (GHG) emissions compared to the other reported microalgae-to-biodiesel chains. For the scope of well-to-wheel (WTW), the optimal microalgae-based energy system reduces 45.77% GHG emissions compared to the conventional diesel process. (C) 2017 Elsevier Ltd. All rights reserved.