A methane (CH4) slip is normally un-avoided during biogas upgrading, and water scrubbing is the most widely adopted upgrading technology. As CH4 is also a key greenhouse gas, such a slip can damage the carbon neutrality of bioenergy and result in a positive emission. In order to eliminate the negative influence, a post treatment to handle the released CH4 is essential. Regenerative thermal oxidation (RTO) is a commercially available air pollution control technology, and it can be used for the post treatment. This paper aims to analyze the technical and environmental performance of RTO for removing CH4 from the waste gas of biogas upgrading by water scrubbing. A three-dimensional numerical model was developed for the thermal flow-reversal reactor (TFRR). CH4 content in waste gas is investigated as the key factor, and the energy consumption, the amount of CH4 elimination and associated CO2 equivalent avoidance are estimated as key performance. It was found that the higher CH4 content benefits maintaining the operation of RTO. With the increase of CH4 content, the energy consumption of CH4 removal decreases. For example, it decreases from 8.05kWh/kg to 1.22kWh/kg when CH4% rises from 0.28% to 0.42%. The case study on a real biogas plant that produces 3909ton biogas per year shows that removing CH4 corresponds to a CO2 equivalent avoidance of 231.38ton/year.