Requirement of a long hydraulic retention time (HRT) for efficient degradation restrains the anaerobic digestion of hydrothermal pretreated sludge. Shortening the HRT can increase the treatment capacity of a plant but may also induce digester instability. This study investigated the impact of HRT on process performance and microbial community by consecutively operating a reactor for 145 days. The HRT was gradually decreased from 20 to 10, 5, and 3 days. The methane yield declined from 0.28 to 0.12 L/g-VSin with this shortening, and acetate concentration increased from 38 to 376 mg/L. Methanoculleus (58%) dominated methanogens at a 20 days HRT. However, the methanogenic structure shifted toward an increased level of Methanospirillum, representing 95% of the total archaea at a 3 days HRT. Microorganisms were almost washed out at the end of experiment. Conclusively, shortening HRTs is a feasible strategy to increase treatment capacity and produce more biogas at existing plants.