The burrowing ocypodoid crab Macrophthalmus japonicus, a major bioturbator on Japanese tidal flats, is classified as a “regenerator”, that reworks the sediment without changing sediment grain distribution. We examined the effects of M. japonicus on abiotic and biotic sediment characteristics through crab exclusion experiments conducted on two adjacent tidal flats in the Tama River, Tokyo Bay, Japan, in 2012 and 2013. Although sediment organic matter content and water content were significantly higher in the exclusion treatment than in the control treatment, the silt-clay content did not differ significantly between them. Microphytobenthos (MPB) biomass was affected negatively by M. japonicus feeding, which caused in a high turnover ratio. The experimental results indicated that M. japonicus decreased MPB biomass and maintained high primary production without changing the sediment grain size distribution. This suggests that “regenerators” affect mudflat abiotic and biotic sediment characteristics in a different manner from other types of bioturbators.