The Yellow River is the largest river in north China which greatly affects the environment of Bohai Sea. The freshwater input and suspended sediments have sustained the morphology and ecology of the river mouth, located in the northeastern modern Yellow River subaerial delta and was formed after the Yellow River shifted again at the north bank of the Qingshuigou course in June,1996. The water and sediment discharge regulation (WSDR) project has been carried out since 2002 by artificially releasing a large amount of water in a short time, which would affect the invertebrate community somewhat to some extent. In order to know the community structure and its seasonal changes of invertebrate community, the characteristic such as species composition, dominant species, biomass distribution, diversity, and community similarity were studied. Survey were conducted in May, June, early July, late July, August and September, 2012. In the investigated area, 3 sections of 15 sample stations were set up. The distance of the estuary mouth to section A, section B and section C was 10, 20 and 40 km respectively. The 15 stations were radial distributed in the survey area. Data were collected using a beam trawl with a 2.5 m width and a 2 cm net mesh. The trawling speed was ~3 knots and each tow lasted ~30 min. The results showed that a total number of 45 species, which belongs to 9 orders, 29 class and 39 genus, were collected. The number of species was between 28 and 35 in each survey. Diogenes edwardsii, were the main species in Huanghe Estuary. Gastropods (a total biomass of 8.4% to 45.8%) and crabs (10.8%–58.6%) were the dominant category of invertebrate by biomass. The trends of seasonal change of biomass and abundance were most similar. Biomass was highest in August and abundance was highest in early July. The Shannon-Wiener diversity index was between 1.482 (in May) and 1.719 (in June). The results of Bray-Curtis similarity and ANOSIM showed that community was more similarly in the adjacent surveys. But the community in May and June was low similarly with that in August and September. According to the results, we can draw the following conclusions: 1) The community was mainly dominated by small low-valued species. Compared with 1980s, the quality of invertebrate resources was further decline. 2) The seasonal distribution of biomass changed significantly compared with 1980s. 3) The biomass and diversity in section B was more fluctuant and irregular than that in section A and C. 4) Community structure of invertebrate was affected somewhat by WSDR project. But the community replacement was not affect significantly by WSDR. Further research, including the environmental factors and other sample methods, should be utilized.