This study investigated mechanism of process imbalance of long-term anaerobic digestion (AD) of food waste (FW) and role of trace elements (TEs) in maintaining process stability. AD of FW was strongly inhibited by volatile fatty acids (VFA, mainly propionate). The deficiency of essential TEs in FW was the fundamental reason. TEs contents in digester gradually decreased with regular substrate feeding and digestate discharge, which greatly limited growth and metabolism of hydrogenotrophic methanogens and Methanosarcina. Finally, Methanosaeta replaced Methanosarcina and became dominant methanogen and hydrogenotrophic methanogens almost disappeared accompanied by declining methanogenic community diversity, which greatly suppressed ecological functions of methanogens and led to propionate inhibition. TEs supplementation eliminated all factors causing process imbalance and significantly enhanced process stability by maintaining strong ecological functions of methanogens via stimulating dominant growth of Methanosarcina (relative abundance between 67.2% and 87.5%), sustaining stable relative abundances of hydrogenotrophic methanogens (about 10%) and enhancing methanogenic community diversity.