Integrated sewage treatment system (ISTY) is a new technology for rural domestic sewage treatment. In the ISTY, the carbon source in the denitrification stage is often insufficient, affecting the denitrification efficiency. In order to improve the denitrification efficiency, several commonly available agricultural wastes, peanut shell (PS), sawdust (SD), peat (PT), and their mixtures (MT), were selected as supplementary carbon sources in the denitrification stage of ISTY to study the denitrification efficiency. Results show that PS exhibited a high carbon release capacity. PS released an enormous amount of carbon in 144 h, and the cumulative total organic carbon was 41.99 ± 0.7 mg/(g·L). The optimum carbon source dosage was 3 g/L, the nitrate removal rates of PS exceeded 95% after 48 h, and the denitrification rates were 9.35 mg/(g·L), which were 63.92% higher than that of the control group. After running the ISTY for 120 h, and with PS as supplementary carbon sources, the removal rate of TN increased from 29.76% to 83.86%. At the genus level, the dominant denitrifying bacteria in ISTY, after adding PS, were Pseudomonas and Cupriavidus, accounting for 78.68%, an increase of 72.90% compared with the control group. This evidence suggested that PS can obviously enhance the denitrification efficiency of the ISTY as a supplementary carbon source.