<p><strong>Abstract.</strong> Microorganisms in sediments play an important role in C-, N- and S-cycles by regulating forms and contents of these elements. The coupled system or synergistic reaction among three elemental cycles can effectively alleviate the pollution of C, N, and S in sediments. However, ecological processes coupling C-, N- and S-cycles in sediments are still poorly understood. In order to understand the ecological processes mediated by microorganisms living in river sediments, a total of 135 sediment samples were collected from Huaihe River and its branches located in the Northern of Anhui Province, the abundance of functional marker genes (<i>mcrA</i>, <i>pmoA</i>, <i>cmo</i>, <i>amoA</i>, <i>hzo</i>, <i>nirK</i>, <i>nirS</i>, <i>nosZ</i>, <i>dsrB</i>, <i>aprA</i>), involving in C-, N- and S-transformation, were determined by <i>q</i>PCR. The correlation among functional genes from 135 river sediment samples was calculated. We supposed that the correlationship among functional genes could be used as a reference index speculating the coupled systems of C-N-S in this reasearch, then the distinct coupling relation of C-N-S was revealed, and probable genetic mechanisms were also expounded based on the hypothesis. The study found that <i>amoA</i>-AOA and <i>dsrB</i> possibly played a secondary role, while S-functional gene (<i>aprA</i>), C-functional gene (<i>mcrA</i>) and N-functional gene (<i>hzo</i>) were the key functional genes that participate in the coupled processes in the elemental biogeochemical cycle. The results also demonstrated that C, N might have combined effects on the coupling of carbon, nitrogen and sulphur transformation.</p>