The viability of hydrothermal pretreatment (HTP) to improve the efficiency of biogas production from municipal solid wastes (MSWs) is uncertain because there is always a trade-off between organic matters hydrolysis and recalcitrant melanoidins formation when applying HTP on different solid wastes. In this study, MSWs including waste activated sludge, fruit and vegetable residues, and kitchen wastes, with and without HTP were digested in the one phase and two-phase anaerobic digesters, respectively. Although the specific biogas production of MSWs in two-phase anaerobic digestion was significantly enhanced by HTP, no benefit could be found in one-phase anaerobic digestion because of the melanoidins formation. The specific biogas production of hydrothermally pretreated MSWs was much higher in two-phase anaerobic digestion (0.71 L biogas/g VSadded) than that of MSWs in one-phase anaerobic digestion with or without HTP (0.53 L and 0.55 L biogasig VSadded) when the butyric acid type fermentation dominated in the acidogenic phase. These findings indicated that the recalcitrant melanoidins formed in the HTP process were probably removed in the acidogenic digester. Differing from previous study, mixed-acid type fermentation, rather than ethanol type fermentation, was observed in the acidogenic digester fed with hydrothermally pretreated feedstock when pH was adjusted in the range of 4.0-4.5 with high oxidation reduction potential values of 49-97 my. The succeeding specific biogas production of mixed-acid type feedstock was only 0.59 L biogas/g VSadded, which was lower than that of the butyric acid type feedstock. Microbial community structure was independent of the pH valties and was substrate-specific in the acidogenic digesters. In the acidogenic digester with the HTP substrate, the phylum Firmicutes and Bacteroidetes increased, thereby possibly resulting from the increased content of soluble sugar and proteins in the HTP feedstock. Energy balance estimation of the four defined scenarios indicated that the combined HTP and two-phase AD in the MSWs treatment can achieve higher net energy output by 50.5-97.4% compared to the other three scenarios. This enables the combined process of HTP and two-phase AD to be a promising alternative way in the treatment of feedstock rich in protein and sugar. (C) 2016 Elsevier Ltd. All rights reserved.