An Illumina-based next-generation sequencing was employed to characterise the sediment microbiome adjacent to coastal industrial and tourist cities, Taizhou and Xiamen, in China, and their associations with chemical pollution were explored. The results indicated that chemical pollution of sediments from Taizhou was higher than that from Xiamen. The number of sediment bacterial genera was negatively (Taizhou) or positively (Xiamen) correlated with offshore distance, owing to shifts in the primary and secondary status of organic matter and chemical pollutants for the promotion or inhibition of the sediment microbiome. The total number of the operational taxonomic units (OTUs) in sediments from Taizhou was larger than from Xiamen, while the number of core OTUs was smaller indicating that Taizhou had more impact on core microbes in sediments than Xiamen. This study suggests that chemical pollutants and organic matter result in different co-regulation of the off-shore sediment microbiome of coastal industrial and tourist cities.