The addition of trace elements to aid anaerobic digestion has already been widely studied. However, the effects of rare trace elements on anaerobic digestion remain unclear. In this study, the effects of Mo, Se and Mn on anaerobic digestion of rice straw were explored. The results showed the methane yield increased by 59.3%, 47.1% and 48.9% in the first 10 days following addition of Mo (0.01 mg/L), Se (0.1 mg/L) and Mn (1.0 mg/L), respectively. Toxic effects and the accumulation of volatile fatty acids (VFAs) were observed when the Se, Mo and Mn concentrations were greater than 100, 1000 and 1000 mg/L, respectively. The half-maximal inhibitory concentrations (IC50) for Se, Mn and Mo were 79.9 mg/L, 773.9 mg/L and 792.3 mg/L, respectively. The addition of trace elements has changed the bacterial structure of the bacteria, which in turn has affected the digestion performance.