<p>Limited research on sulfur-metabolizing microorganisms and their functional genes in shale gas wells has hindered a comprehensive understanding of corrosion mechanisms in gathering pipelines. We conducted an analysis of the physicochemical water parameters at various stages, specifically examining clear water, flowback liquid, and produced water. Concurrently, we investigated the microbial community structure and examined the composition of sulfur metabolism function genes. The results indicate that, in the clear water sample, <i>Nitrincola</i> (CysP) constituted 6.52% and <i>Desulfuromonas</i> (CysA) 3.11% as the main genera. In the return flow stage, <i>Marinobacterium</i> and <i>Marinobacter</i> played a major role (CysA, CysI and CysJ). In the initial production stage, <i>Shewanella</i> (CysN and CysD) had a high abundance, reaching 34.08%. Two months after the start of production, <i>Desulfuromonas</i> (CysA) and <i>Hyphomonas</i> (CysH) were dominant, with abundances of 2.66% and 0.01%, respectively. Notably, the concentrations of S²⁻ and SO₄²⁻, were found to be closely associated with the variations in these sulfur-metabolizing functional genes. During the late flowback and production phases, these microorganisms exerted the most significant influence on pipeline corrosion. In summary, this study elucidated the dynamic changes in sulfur-metabolizing microorganisms and their functional genes in water samples collected at various stages of shale gas extraction. By analyzing the role of these sulfur-metabolizing functional genes in the corrosion processes of gathering pipelines, the research offers a novel perspective on developing anti-corrosion strategies for shale gas pipelines.</p>