In the context of global warming and carbon neutrality, reducing greenhouse gas emissions is fundamental to achieving sustainable development. As an important greenhouse gas, methane has a much stronger warming effect than CO2, and studies have demonstrated that anaerobic oxidation of methane (AOM) is important for global methane emissions. This paper systematically investigated the AOM potential and microbial community response to the input of SO42− in the three typical salt marsh soils of the Yellow River Delta: Reed, Suaeda salsa, and Tamarisk, using SO42− as the electron acceptor and a combination of indoor anaerobic culture and high-throughput sequencing. The results showed that after adding an appropriate concentration of SO42−, the AOM potential was significantly promoted in Tamarix soil (p < 0.05) and significantly inhibited in Reed and Suaeda salsa soil (p < 0.05); soil AOM potential and SO42− input concentration and background values were correlated. At the microbial level, SO42− input affected the abundance of some microorganisms. At the phylum level, the relative abundance of Proteobacteria was increased in Suaeda salsa soil, decreased in Tamarisk soil, and did not change significantly in Reed soil; that of Crenarchaeota and Desulfobacterota was significantly increased in Tamarisk soil. At the genus level, Methylophaga, Methylotenera, and Methylomonaceae became the dominant populations, and it can be inferred that these bacteria are involved in the anaerobic oxidation of methane after the input of SO42−. This study will be of great significance to the mechanistic study of AOM and the conservation of microbial diversity in the Yellow River Delta Coastal Wetland, as well as provide a scientific basis for CH4 reduction in coastal wetlands.