Thermophilic anaerobic digestion (AD) offers many benefits for food waste treatment but is seldom adopted in industrial plants due to instability issue, particularly under higher loading conditions. This study thus conducted a 160-day continuous operation of a pilot-scale thermophilic AD system on-site. Results from the experiments showed that the system could operate under relatively lower loading but failed when the loading reached up to 5.69 kg·COD/(m3·d). Volatile fatty acids increased to 6000 mg/L at the corresponding hydraulic retention time of 15 days. Trace elements were then introduced, which restored higher process stability by reducing volatile fatty acids to 400 mg/L. The mass balance and materials decomposition resutls revealed the system’s strong resilience. Methanoculleus (92.52 %) and Methanomassiliicoccus (6.55 %) were the dominant methanogens, a phenomenon rarely observed in similar thermophilic systems. This system may tolerate more stressful conditions, as the loading limits had not been reached with the addition of trace elements.