The sludge production from medium- and small-scale wastewater treatment plants in the Three Gorges Reservoir Region is low and non-stable; especially, the organic content in this sludge is low (near 40% of VS/TS). An integrated thickening and digestion (ISTD) reactor was developed to treat this low-organic excess sludge. After a flow test and start-up experiment of the reactor, a running experiment was used to investigate the excess sludge treatment efficiency under five different excess sludge inflows: 200, 300, 400, 500 and 400 L/d (a mixture of excess sludge and primary sludge in a volume ratio of 9:1). This trial was carried out in the wastewater treatment plant in Chongqing, which covers 80% of the Three Gorges Reservoir Region, under the following conditions: (1) sludge was heated to 38–40 °C using an electrical heater to maintain anaerobic mesophilic digestion; (2) the biogas produced was recirculated to mix raw sludge with anaerobic sludge in the reactor under the flow rate of 12.5 L/min. There were three main results. Firstly, the flow pattern of the inner reactor was almost completely mixed under the air flow of 12.0 L/min using clear water. Secondly, under all the different sludge inflows, the water content in the outlet sludge was below 93%. Thirdly, the organic content in the outlet sludge was decreased from 37% to 30% and from 24% to 20%, whose removal ratio was in relation to the organic content of the inlet sludge. The excess sludge treatment capacity of the ISTD reactor was according to the organic content in the excess sludge.