Acid sulfate soil (ASS) is sensitive to redox fluctuations induced by climate change and human activities. Oxidation of sulfur and sulfide in ASS leads to the release of acid and consequently metals, posing severe hazards to coastal environment, while microbial contribution and response to oxidation is poorly understood. Here we used metagenomic sequencing to delineate the shift in microbial community structures and functional genes in ASS upon exposure to aerobic conditions. Aerobic incubation resulted in significant shifts in microbial communities in both topsoil and parent material. Archaea decreased significantly in the parent material after aerobic incubation. The relative abundance of sulfur cycling genes in the parent material layer was significantly higher than those in the topsoil, and multiple sulfide oxidation genes increased after aerobic oxidation. Metagenomic assembly enabled construction of eight key draft genomes from ASS. Three of them (GS3, GS6 and GT3) are novel strains of Thermoplasmatales, Acidothermales (Acidothermus) and Acidimicrobiales, respectively. Functional gene annotation of these population genomes revealed a dominance of sulfur cycling genes and acid tolerant genes. These findings highlight the microbial response to environmental change and identify the ecological adaptation and survival strategies of microbial communities in acid sulfate soils.