Bacteria play fundamental roles in regulating marine ecosystem functioning, yet the understandings towards how bacterial functions and community structure are affected by the resource stoichiometry (quantity and quality) are scare. Here, with huge quantity of biological samples collected aboard from East China Sea, we utilized DNA barcoding method and chemical analysis to acquire heterotrophic bacterial community data and resource elemental ratio, that is Carbon: Nitrogen: Phosphorous (C: N: P), respectively, and further compared these with bacterial functions measured on board. Interestingly, bacteria community diversity decreased significantly with the organic resource availability, and exhibited a hump-shaped patterns with C:N ratio. However, no relationship was found between bacteria community diversity and C: P and N: P ratio. These findings supported the prediction of Resource ratio theory and further suggested Carbon and Nitrogen resources act as two main limiting factors driving the competition outcome of bacterial community. Furthermore, bacterial functions such as production and growth efficiency were also significantly affected by the organic resource stoichiometry, indicated by increased production and growth efficiency in lower C: N ratio. Our results highlighted the importance of organic resource stoichiometry in regulating bacteria community structure and functions in marine ecosystem.