Humic acids (HAs) are important byproducts of anaerobic digestion (AD), which have complex structures and dynamic electrochemical activities. However, the effects of HAs on AD process were usually misestimated due to the neglect of the in situ generated HAs and the interaction between HAs and metal ions. This study explored the effects of HAs on AD performance using corn straw as typical “clean” substrate (rare in metals content) via commercial HAs (C-HAs) addition and in-situ-generated HAs (In-HAs) removal. Results showed that C-HAs (1 g/L) addition promoted the maximum methane production rate (Rm) by 20.6%, while In-HAs removal decreased the Rm by 42.7%. Meanwhile, C-HAs showed little effect on the acidification of corn straw but increased the Rm during the methanation of ethanol by 41.6%. Both the C-HAs and In-HAs were rich in surface oxygen-containing functional groups, which enabled them to act as electron shuttles and facilitate the syntrophic methanogenesis. HAs also acted in regulation of syntrophic microorganisms. For instance, C-HAs addition enriched the relative abundances of Cloacimonadia, Spirochaetia, Synergistia and Methanosarcina, while the removal of In-HAs reduced the relative abundances of Spirochaetia and Synergistia. In conclusion, HAs addition to the AD process could be a feasible approach to improve methane production by enhancing direct interspecies electron transfer during AD of lignocellulosic biomass.