This study presents detailed emission of greenhouse gases of using Clean Energy Agriculture System according to a cradle-to-gate life-cycle assessment, including emission from energy use and leak of Biogas. Calculations were done with the PASS software and the covered gases are CH4, N2O and CO2, Total GHG fluxes of amount to 1719.03 kgCO2/day, 39.63 kgCO2/day (2.31%) are from facility house process, 0.19 kgCO2/day (0.01%) are from transport process, 696.72 kgCO2/day (40.53%) are from Anaerobic digestion process, 846.61 kgCO2/day (49.25%) are from Heating and cooling system, 135.88 kgCO2/day (7.90%) are from Fertigation production process. The results suggest that for effective reduction of GHG emissions from Facility house using clean energy. Reduction targets should address both the production process as defined by IPCC sectors and the consumption process. An LCA assessment as presented here could be a basis for such efforts.