A pilot-scale experiment of natural rubber processing wastewater treatment was conducted using a combination system consisting of a two-stage up-flow anaerobic sludge blanket (UASB) and a down-flow hanging sponge (DHS) reactor for more than 10 months. The system achieved a chemical oxygen demand (COD) removal efficiency of 95.7% ± 1.3% at an organic loading rate of 0.8 kgCOD/(m3.d). Bacterial activity measurement of retained sludge from the UASB showed that sulfate-reducing bacteria (SRB), especially hydrogen-utilizing SRB, possessed high activity compared with methane-producing bacteria (MPB). Conversely, the acetate-utilizing activity of MPB was superior to SRB in the second stage of the reactor. The two-stage UASB–DHS system can reduce power consumption by 95% and excess sludge by 98%. In addition, it is possible to prevent emissions of greenhouse gases (GHG), such as methane, using this system. Furthermore, recovered methane from the two-stage UASB can completely cover the electricity needs for the operation of the two-stage UASB–DHS system, accounting for approximately 15% of the electricity used in the natural rubber manufacturing process.