To investigate whether thermodynamic calculations of anaerobic digestion processes can be applied to the early warning for unstable anaerobic digestion, a group of semi-continuous digesters fed with an energy crop (Hybrid Pennisetum) were operated via a step-wise increase in the organic load rates until overload occurred. Traditional early warning indicators, such as biogas production and content, pH, alkalinity, and volatile fatty acids as well as the methane/carbon dioxide (CH4/CO2) and volatile fatty acid/alkalinity ratios, were regularly monitored during the process. The Gibbs free energy changes (ΔG) of the methanogenesis phases of valerate, butyrate, and propionate were calculated based on Nernst and Van’t Hoff equations. The results demonstrate that ΔG of the three syntrophic methanogenesis phases can be used as an early warning indicator for unstable anaerobic digestion, indicating anaerobic digestion failure (ceased biogas production) up to 21 days in advance, that is, 1–8 days earlier than some other indicators.