A comparison was conducted between pre-culture bacteria (PCB) and heat treatment anaerobic granular sludge (HTAGS) for hydrogen production, and it was found that hydrogen molar yield (HMY) of PCB was 21–35% higher than that of HTAGS. The addition of biochar increased hydrogen production in both cultivation methods by acting as an electron shuttle to enhance extracellular electron transfers of Clostridium and Enterobacter. On the other hand, Fe3O4 did not promote hydrogen production in PCB experiments but had a positive effect on HTAGS experiments. This was due to the fact that PCB was mainly composed of Clostridium butyricum, which could not reduce extracellular iron oxide, resulting in a lack of respiratory driving force. In contrast, HTAGS retained a significant amount of Enterobacter, which possess the ability of extracellular anaerobic respiration. Different pretreatment methods of inoculum resulted in significant changes in the sludge community, thus exerting a noticeable impact on biohydrogen production.