Physical structures of sludge are critical factors determining the performance of the anaerobic digestion process, especially for the rate-limiting step, methanogenesis. Thus, to evaluate the effect of granular physical structure on methanogenesis and methanogenic community variation, intact and disintegrated granules were applied as inocula with formate, hydrogen and acetate as sole substrates in batch reactors. Kinetics results revealed that the physical structure of sludge had little impact on methane yield potential from three substrates, while a significantly different impact on methanogenesis rates of formate, hydrogen and acetate. The methanogenesis rate of formate in disintegrated granules was higher than that in the intact granular system, the methanogenesis rate of H2/CO2 in the intact granular system was higher than that in the disintegrated granules and the methanogenesis rate of acetate was similar with the in intact and disintegrated granular systems. Besides, in both intact and disintegrated granular systems, methanogenesis rates of formate were the highest, then followed the H2/CO2 and acetate was the lowest, indicating formate consumption has an advantage over hydrogen in the studied system. A microbial assay indicated that Methanobacteriales, Methanosarcinales and Methanomicrobiales are dominant methanogens on the order level, and the physical structure of granular sludge has little influence on methanogenic communities on the order level but showed significant influence on the species level. It enlightens us that the physical structure of sludge could be considered for regulating the anaerobic digestion via influencing the methanogenesis rates.