Microbial Electrolysis Cells (MECs) are one of the bioreactors that have been used to produce bio-hydrogen by biological methods. The objective of this comprehensive review is to study the effects of MEC configuration (single-chamber and double-chamber), electrode materials (anode and cathode), substrates (sodium acetate, glucose, glycerol, domestic wastewater and industrial wastewater), pH, temperature, applied voltage and nanomaterials at maximum bio-hydrogen production rates (Bio-HPR). The obtained results were summarized based on the use of nanomaterials as electrodes, substrates, pH, temperature, applied voltage, Bio-HPR, columbic efficiency (CE) and cathode bio-hydrogen recovery (C Bio-HR). At the end of this review, future challenges for improving bio-hydrogen production in the MEC are also discussed.