Reducing energy consumption and green house gas emissions is a crucial issue in the cassava starch processing industry. In this study, the integrated system combining livestock, cassava cultivation and cassava production at the same area will lead to both zero emission goal and economic efficiency, a typical example of an effective agro-industrial symbiosis. A heat exchange/recovery system was applied including the economizer, the heat exchanger tank, the biogas tank, and the boiler. The economizer attached to the boiler’s chimney transfers heat from exhaust gases for pre-heating feed water entering boiler. The biogas tank recovers energy from the wastewaters of starch production and livestock farm, and the generated biogas was used as fuel for the boiler. Excess heat from the production was used for evaporating (removal of) NH3 in wastewater flow from the biogas tank, and for heating the biogas system in oder to enhance the efficiency of methane production. A biochar filter was attached to economizer for adsorption of released ammonium, and the biochar after adsorption was combined with sludge from the biogas tank to produce a solid biofertilizer. The energy and exergy efficiency, energy losses, and exergy destruction for heat recovery system were analyzed. The specific energy consumption (SEC) was used to evaluate the overall energy efficiency for cassava starch factory with a capacity of 200 tons/day. The results show that there is a high potential to recyle waste into energy in the cassava starch industry, and the total energy saving and reducing GHG emissions per year of the cassava starch factory were 5.4%/year and 278,773 tons CO2/year, respectively.