The present invention relates to a method for enhancing deep degradation of proteins in sludge. The method includes the following steps: an anaerobic digestion product of excess sludge as a substrate is treated by Van Soest's washing method to obtain the sludge free of easily degradable organics and containing degradation-resistant proteins; then, with the anaerobic digestion product of excess sludge as an inoculum and the sludge free of easily degradable organics and containing degradation-resistant proteins as a substrate, a first-stage microbial electrolytic cell coupled anaerobic digestion system is started for treatment to obtain a microbial mixture related to targeted degradation of the degradation-resistant proteins; with the microbial mixture related to targeted degradation of the degradation-resistant proteins as an inoculum and the anaerobic digestion product of excess sludge as a substrate, a second-stage microbial electrolytic cell coupled anaerobic digestion system is started to obtain the sludge with deeply degraded proteins.