Agrobacterium-mediated genetic transformation is commonly used in dicotyledon plants such as apples. The regeneration ability of the recipient is an important factor in transformation efficiency. Here, the variations in bud regeneration rate (BRR) and the number of adventitious buds (NAB) formed per explant in Malus germplasm accessions with phenological stage were estimated. Both BRR and NAB of explants at the dormancy broken and spring sprouting stages were significantly higher than those at the autumn sprouting stage. The genetic diversity and inheritance of BRR and NAB were evaluated using 153 Malus germplasm accessions and 78 hybrid trees of Jonathan × Golden Delicious. Malus sieversii 31, Liberty, and Smoothee exhibited significantly high BRR (98.33%, 98.33%, and 93.33%, respectively) and a large NAB without vitrification. BRR and NAB linearly correlated with each other but not with callus formation rate. The broad sense heritability of the regeneration rate was 92.16%. The three Malus accessions that had high regeneration ability, and some of their sexual descendants, might be outstanding genetic resources for future genetic transformation.