Carbon capture performance is a key factor determining the chemical energy recovery potential of the high-rate contact stabilization (HiCS) process. However, the mechanisms of organic carbon capture are complex, involving surface adsorption, extracellular adsorption, and intracellular storage. A unique characteristic of the HiCS process is its low sludge residence time (SRT). Unfortunately, the influence of SRT on carbon capture has not been thoroughly studied, especially in terms of the underlying mechanisms. In this study, the microscopic changes in carbon capture performance during the transition from a conventional contact stabilized (CS) system to a high-rate mode of operation were demonstrated using intracellular carbon sources, extracellular polymeric substances (EPS), signaling molecules, and microbial community assays. The results showed that the extracellular carbon adsorption and intracellular carbon storage performance increased, and the microbial community structure changed significantly with converting the CS system to the high-rate operation mode. The enhancement of extracellular carbon adsorption performance mainly relied on the growth of EPS, which was accomplished by the strong growth of the relative abundance of the dominant bacterial group Cloacibacterium within the HiCS system, offsetting the negative effect produced by the decline of acyl-homoserine lactones. 98 mgCOD/gSS, 343 mgCOD/gSS, and 500 mgCOD/gSS of polyhydroxyalkanoates (PHAs) per sludge unit were obtained at SRT-24d, 8d, and 2d, respectively, suggesting that the HiCS system is more advantageous for rapid PHAs production.