The integrated system of anaerobic digestion and microbial electrolysis cells (AD-MEC) was a novel approach to enhance the degradation of food waste anaerobic digestate and recover methane. Through long-term operation, the start-up method, organic loading, and methane production mechanism of the digestate have been investigated. At an organic loading rate of 4000 mg/L, AD-MEC increased methane production by 3-4 times and soluble chemical oxygen demand (SCOD) removal by 20.3% compared with anaerobic digestion (AD). The abundance of bacteria Fastidiosipila and Geobacter, which participated in the acid degradation and direct electron transfer in the AD-MEC, increased dramatically compared to that in the AD. The dominant methanogenic archaea in the AD-MEC and AD were Methanobacterium (44.4-56.3%) and Methanocalculus (70.05%), respectively. Geobacter and Methanobacterium were dominant in the AD-MEC by direct electron transfer of organic matter into synthetic methane intermediates. AD-MEC showed a perfect SCOD removal efficiency of the digestate, while methane as clean energy was obtained. Therefore, AD-MEC was a promising technology for deep energy transformation from digestate.