The invention discloses a technique for treating fermentation wastewater by a microbial fuel cell, and relates to a technique for treating wastewater. The method comprises the steps as follows: with conductive glass, carbon cloth or a carbon felt as electrode materials, active groups, polyelectrolyte multilayer films or nanoparticles/polyelectrolyte multilayer films are respectively modified on the electrode materials by an alkaline hydrolysis method, an acid hydrolysis method and a layer-by-layer self-assembly technique; the series materials are applied to an anode of a microbial fuel cell reaction device to treat the fermentation wastewater; with sodium acetate and lotus pond sludge as substrates, a microbial fuel cell system with a relatively high electricity generating rate, relatively good chemical oxygen demand (COD) removal effects and relatively high coulombic efficiency is obtained. The microbial fuel cell system is good in process repeatability, safe and reliable; the fermentation wastewater is treated; meanwhile, a relatively high electricity generating quantity and a relatively high electricity generating rate are achieved; the problems that the traditional microbial fuel cell is low in electricity generating efficiency and low in sewage COD removal rate are effectively solved; and the technique has a good industrial application prospect.