Deterioration of anaerobic digestion can occur with the presence of polyacrylamide (PAM) in waste activated sludge, but the information on alleviating this deterioration is still limited. In this study, the simultaneous alleviation of negative effect of PAM and improvement of methane production during anaerobic digestion was accomplished by microwave pretreatment. Experimental results showed that with the microwave pretreatment times increased from 0 to 12 min, the biochemical methane potential of PAM-flocculated sludge (12 g PAM/kg total solids) asymptotically increased from 123.1 to 242.5 mL/g volatile solids, hydrolysis rate increased from 0.06 to 0.13 d−1. Mechanism analysis indicated that the microwave pretreatment accelerated the release and hydrolysis of organic substrates from PAM-flocculated sludge, facilitated the breaking of large firm “PAM-sludge” floccules, and benefited the degradation of PAM, which alleviated the PAM inhibitory impacts on digestion and meanwhile provided better contact between the released organic substrates and anaerobic bacteria for methane production.