Slug bubbling in single deck flat sheet membrane bioreactor (FSMBR) is effective in controlling membrane fouling. Here the primary focus is on the employment of the slug bubbling method, with its more economical air consumption, to a double-deck large-scale FSMBR with 100 membrane plates on each deck. The analysis of a new design concept shows that sufficient hydrodynamic effect could be induced by a novel economical three-stage slug aeration process of formation-breakup-reformation. Computational fluid dynamics simulation was applied to examine both the development of the slug bubble and especially its reformation. It was found that the combination of a gap between two decks of 400 mm with an air velocity of 16 m/s was an optimal condition to achieve good hydrodynamic conditions in both decks. The corresponding SADm is 0.098 Nm3m−2 hr−1, which is a reduction of 66% compared to the most advanced single deck FSMBR.