Abstract: Malus prunifolia Borkh is a kind of nice arbor which holds flower and fruit ornamental merits, whose market needs increase year by year. How to clone mass saplings of M.prunifolia is an urgent issue in its industry. For years, some rooting traits of Malus spp. have been explored at cell level, such as cutting soil material, exogenous hormones, cutting season and other factors’ effects on the abilities of taking roots, as well as the anatomical characters on the rooting of the cuttings. However, the studies on changes of soluble proteins in the process of striking root of M.prunifolia are still not reported. Therefore, to explore this matter helps to establish theoretical basis for cloning mass saplings of M.prunifolia. By applying the techniques of SDS-PAGE & ELISA, this paper studied and explored the relationship between rooting and the variances of both soluble proteins and endogenous plant hormones in the process of striking root cutting of M.prunifolia. The results showed that: during the cutting procedure, the soluble proteins of 83, 72, 65, 52, 43, 39, 31, 28, 26, 22 ku were related to rooting. The soluble proteins in 65, 39, 26, 22 ku existed when the adventitious roots′ primordium differentiated. Furthermore, they disappeared when the cuttings generated adventitious roots. While rooting was in proceeding, some new kinds of soluble proteins like 43, 31, 28 ku that were good for promoting new adventitious roots generated. It seemed that another soluble protein 52 ku in striking roots had some disadvantages to the adventitious root primordium differentiation. Moreover, in the B treatment, soluble proteins 83 ku & 72 ku emerged which had some advantages to both the quantities and qualities of adventitious roots. During the process of striking root, endogenous plant hormones ZR under A & B treatment kept at a high level all the time, whereas CK was relatively low. IAA played a concurrent role other than magistral ones. GA played an important role in adventitious roots’ primordium differentiating and it correlated with the synthesis of 28 ku soluble protein. ABA content in treated cuttings was lower than that of CK. Among them, cuttings under B treatment held lowest record. The conclusion is that different exogenous hormone treatments affect the variances of endogenous hormones of the cuttings of M.prunifolia. Furthermore, they also influenced the types, quantities and arisen time of soluble proteins in the cuttings of M.prunifolia.