Microcosms were setup to investigate the possible impact of copper exposure on bacterial community structure and function in sediments of Jiaozhou Bay, China, by culture-independent microbial ecological techniques and community-level physiological profiling. Bacterial 16S rDNA libraries indicated that proportion of the bacteria in phyla Chloroflexi and Acidobacteria decreased, but that of Gammaproteobacteria and Planctomycetes slightly increased in copper-treated sediment. Denaturing gradient gel profiles showed that bacterial communities in control and copper exposed sediments developed into different directions, while the copper exposure did not change the pattern of ammonia oxidizing bacterial community. Microbial community-level physiological profiling revealed an obvious response to copper dosage. The copper pollution caused an acute decrease of carbon utilizing ability as well as bacterial functional diversity; the number of culturable heterotrophic bacteria was reduced by 90%. This study demonstrated that high copper input would obviously reduce culturable bacterial counts and seriously impact bacterial community function in marine sediments.