Due to the potential negative impact on human health and environmental safety of medical waste, it is of great significance for numerous small and medium medical institutions far away from cities or inland to dispose of a small amount of medical waste harmlessly on the spot. However, there still lacks small-scale packaged technology for the clean and high-efficiency treatment of medical waste, so it is difficult to implement the onsite hazard-free reduction disposal of medical waste. In view of some combustion and flue gas treatment problems confronted in the harmless onsite disposal of a small amount of medical waste, this work designed and experimentally verified an integrated decoupling incineration treatment system suitable for the decentralized disposal of medical waste by using the so-called decoupling combustion technology. The results showed that the decoupling incinerator could facilitate the high-efficiency and stable combustion of medical waste and the suppression of emissions of nitrogen oxides (NOx) and dioxins (PCDD/Fs). The small flue gas purification facility based on two-stage wet desulphurization technology enabled rapid cooling of flue gas to avoid the secondary generation of dioxins and simultaneous removal of acidic substances and particulate matter (PM). Treating typical medical waste blending in the small integrated decoupling incineration system, the emissions of NOx, SO2, PM, CO, and PCDD/Fs could be lower than 123, 1.8, 38, 53 mg/m3, and 0.31 ng I-TEQ/m3 on the 11vol% O2 basis, respectively. The newly-developed small medical waste incineration treatment system featured a compact configuration structure and high purification efficiency because of its integrated design of decoupling incinerator and purification equipment so that it can meet the need for onsite clean disposal of daily medical waste in the decentralized medical institutions.