Using the newly developed Ludox-QPS method, we investigated the community composition, abundance and biomass, and distribution of benthic diatoms, ciliates and heterotrophic microflagellates (HMF) and meiobenthos in combination with the analysis of benthic environmental variables at ten stations in the Changjiang (Yangtze) Estuary and East China Sea in April 2011. The benthic diatoms were dominant both in the abundance (5.92×10⁴ ind/10 cm²) and biomass (83.29 μg C/10 cm²), followed by benthic ciliates (abundance: 1036 ind/10 cm², biomass: 3.33 μg C/10 cm²) and HMF (4451 ind/10 cm², 2.51 μg C/10 cm²). The abundance of meiobenthos in the upper 8 cm of sediments was (1947±849) ind/10 cm² and the biomass was (49.01±22.05) μg C/10 cm². Among the 11 meiobenthos groups identified, nematodes accounted for 90% of the total abundance and 37% of the total biomass. The biomass of benthic diatoms was distinctly higher in the coastal region than that in the offshore area, while the distribution pattern of benthic ciliates, HMF and meiobenthos was exactly opposite. On average 76% of diatoms and 80% of nematodes were distributed in the 0-2 cm sediment layers, while the respective proportions were only 1% and 6% in the 5-8 cm layers. Statistical analyses showed that the standing crops of benthic diatoms had significantly positive correlation with sediment chlorophyll-a contents and weak positive correlation with bottom water temperature, and benthic protozoa and meiobenthos might be structured by the interaction of multiple rather than single environmental variables. Our data indicate that the density of benthic diatoms in the sediments was very high, about two orders magnitude higher per unit volume than that in the water column of the Changjiang Estuary and East China Sea, where a great proportion of sediment chlorophyll a was contributed by benthic diatoms. The benthic ciliate abundance in the upper 8 cm of sediments were 30 times higher and the biomass was 40 times higher than those in the water column of upper 30 m of the Changjiang Estuary and East China Sea. Although the biomass of ciliates was lower than that of meiobenthos, their production was up to 3 times higher than that of meiobenthos. The relative turnover rate of heterotrophic microflagellates might even be much higher due to their small size. The high standing crops and production of benthic protozoa and meiobenthos indicate their important role in the ecosystem structure and function of the Changjiang Estuary and East China Sea.