Ten varieties of potted apple were subjected to thermotherapy coupled with in vitro meristem culture and in vivo shoot‐tip grafting. Using reverse transcription–polymerase chain reaction assays prior to treatment, all treated apple varieties were infected by more than two viruses, and nine of ten varieties were infected by Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV). After treatment, the survivals of the two methods were more different. Total survival rates of the seven apple varieties (YF9, XYF3, X2001, GL, HF, A123 and ZZ5) treated by thermotherapy coupled with in vitro meristem culture were 25.9% (14/54). The survival rate of YF9, XYF3, X2001, GL, YF6, JJ and XNH treated by thermotherapy coupled with in vivo shoot‐tip grafting was from 33.3% to 75.0%, and the average rate (63.0%, 34/54) was twice than that of meristem culture. The virus‐free apple plants were acquired only from in vitro variety HF and A123, and the elimination rate of A123 was highest, up to 71.4% (5/7). Fourteen apple survival grafting plants from five varieties (YF9, XYF3, X2001, YF6 and XNH) were detected virus‐free. The average elimination rate of the meristem culture and shoot‐tip grafting was very close, 42.9% (6/14) and 41.2% (14/34), respectively.