Batch anaerobic digestion (AD) using food waste (FW) as a substrate with mono trace element (TE) supplementation of Fe, Co, and Ni was simultaneously carried out under mesophilic conditions. The AD of food waste without TE, was severely inhibited by volatile fatty acid (VFA) accumulation. TE supplementation improved VFA conversion and methane production, with Ni and Co groups showing better enhancements to the AD process. The optimal group received 5 mg/L Ni supplementation, increasing methane production from the 211.3 to 489.22 mL g⁻¹ VS. The fermentative microbes in TE groups are strengthened by improving the abundance of Firmicutes while decreasing Proteobacteria. Methanosarcina replaced Methanobrevibacter as the dominant methanogen in the TE supplementation groups. The genera Thermovirga and norank_f_Synergistaceae, which could be syntrophic co-culture with hydrogenotrophic methanogens, were distinctly improved in the Ni and Co groups. This study could shed more lights on understanding the TE supplementation effects in AD.