The process of microbial extracellular electron transfer (EET) is an important driving force of element cycling and energy exchange in epigeosphere. While the previous studies focused on the interaction between soil particles and ions, recently, the biogeochemical processes of the EET among microbe–humus–mineral received widespread attention. The current EET studies enlightened us with new insights into the epigeosphere from the perspectives of chemistry and microbiology. Since microbes, humus and minerals are very essential factors of the biogeochemical processes on earth surface system via their interactive redox reactions, the main aim of this review is to reveal the detailed mechanism of the EET among microbe–humus–mineral and illustrate their biogeochemical significances on the earth surface system. The paper introduces, first, pathways via which electrons flow from inside to outside of a microbial cell, and then, two pathways via which electrons transfer from the surface of microbes to humus and minerals: (i) direct electron transfer, including direct contact and nanowires; (ii) indirect electron transfer mediated by humus, including “electron shuttling processes” and processes of bonding between humus and membrane c-type cytochromes. In this review, based on the key processes and key factors of the thermodynamics, energy transport processes of the whole EET chain of the microbe–humus–mineral system was discussed on a theoretical basis. The importance of redox state of c-type cytochromes on EET was highlighted through those discussions, which suggests that the standard redox potential (E⁰) and electron transfer capacity (ETC) of humus play dominant roles in the humus-mediated electron shuttling processes. Furthermore, the mass transfer and reaction rates under molecule level are also analyzed using a kinetic approach, which suggests that mediated nanowire-network-mediated electron transfer might be the most efficient way for facilitating EET processes. In this field, there are several new technical means available to solve the key scientific issues, including: (i) spectroelectrochemistry, combining electrochemistry and spectroscopy, is a useful approach for correlating thermodynamics and kinetics; (ii) molecular biology techniques are essential for recognizing the functional proteins responsible for EET processes; (iii) high-resolution imaging techniques are very conducive to the study on micro-structure of the nanowires; and (iv) time-resolved techniques are essential to determination of the rapid reaction occurring in the EET processes. To sum up, the future studies in this field should encompass the following four aspects: (i) studies related to extracellular respiring bacteria, which may help build a complete picture of the bacterial community, and will be helpful for the reorganization of other unknown strains; (ii) The summary on the functions of the proteins responsible for EET will help understanding their roles in this EET process; (iii) The discussion on humus and minerals, especially their structure, can improve the understanding of their functional mechanism and highlight their microbial ecological significances; (iv) The modeling of EET processes from thermodynamics and kinetics can provide a quantitative understanding of the intrinsic factors controlling EET processes.