Laboratory experiments using an undisturbed sediment core were conducted to explore the effect of organic matter(humic acid)on the nitrogen transformation and the nitrate reduction pathway in the hyporheic zone of Lake Taihu. Results show that, when only the nitrate was input along with the downwelling flow, nitrate reduction rates were 0. 087-0. 186 μg/(cm³·d)with an average of 0. 162 μg/(cm³·d), and the nitrate apparently accumulated in the hyporheic zone. Both the humic acid and the nitrate input along with hyporheic flow gradually promoted a reduction environment in the hyporheic zone within 21 days with Eh of below -200 mV. Nitrate reduction was greatly enhanced under this condition with an average reduction rate of about 0. 220 μg/(cm³·d)from 0. 092 to 0. 251 μg/(cm³·d). These indicated that added humic acid substantially promoted the nitrate reduction process. At a shallow depth of the hyporheic zone(0-22. 5 cm), the contribution of denitrification to the nitrate reduction reached more than 90%, indicating that the denitrification was the main pathway of nitrate reduction. At the deep depth of the hyporheic zone(22. 5-45. 0 cm), due to the deficient nitrate source, the contribution of nitrate reduction to the whole hyporheic zone accounted for less than 10%, and the denitrification accounted for about 39. 5%. Dissimilatory nitrate reduction to ammonium, as a secondary pathway of nitrate reduction, was obviously influenced by organic matter content, and its contribution to nitrate reduction decreased from 14. 0% to 2. 7% when organic matter concentrations decreased from 6. 92 mg/L to 3. 32 mg/L. Overall, supplementary organic matter was helpful for the nitrate reduction mainly by denitrification particularly at the shallow depth of hyporheic zone, playing a great role on the cycling and removing of carbon and nitrogen in a lake aquatic system.