In this study, we evaluated the effectiveness of thermotherapy in eliminating apple rubbery wood virus 2 (ARWV-2) in six infected apple varieties collected from regions in China. These plants were subjected to high-temperature treatment, followed by excision of shoot tips, which were subsequently grafted onto the rootstock. All varieties exhibited high thermostability, but the survival rates (average: 30.5%) of the shoot tips varied markedly. The regenerated plants were tested using semi-nested PCR; the results showed that the ARWV-2 elimination efficiencies differed greatly among the varieties. The elimination rates were > 80% for Baxianzaofu and Ruixue and < 50% for HL, Longkou no. 3, and Yishuihong. Notably, all surviving Longkou no. 3 plants remained infected with ARWV-2. The average ARWV-2 elimination efficiency was 44.3%, closely aligning with that of the apple stem pitting virus and apple stem grooving virus. This suggests that the presence of ARWV-2 may influence the ability of certain varieties to yield virus-free germplasm. Moreover, analysis of the ARWV-2 sequences from Baxianzaofu, Ruixue, Longkou no. 3, and Yishuihong revealed that the elimination rate exhibited minimal correlation with the virus diversity. The consistency and identity of the different variants within the same isolates or among the four isolates were high. Our findings can serve as a valuable foundation for developing treatment strategies to address ARWV-2 infections.