The wild apple tree Malus sieversii is a tertiary relict species and a key ancestor of the commonly cultivated apple trees today. In recent years, many M. sieversii individuals have died or have severe dead branches. Whether branch death would lead to the change in nutrient stoichiometry of M. sieversii remains unclear. In this study, the nitrogen (N), phosphorous (P), and potassium (K) stoichiometric traits of M. sieversii individual trees with different proportion of dead branches divided into three classes (Class I [< 20%], Class II [40–60%], and Class III [> 80%]) during annual growth period, elemental scaling relations, and the possible influencing factors were systematically analysed. Leaf N, P, and K decreased during growing season, and N and P did not show significant differences among the three classes; however, the Class III wild apple trees had the lowest K contents in both photosynthetic and reproductive organs. Flowers had higher P and K contents than leaves, whereas fruits had low N content. The growth of M. sieversii was always limited by N due to low N:P ratio and N resorption efficiency. The scaling exponents of leaf N–P, N–K, or P–K among the three classes did not show any significant differences, revealing an inherent property of M. sieversii. Most soil variables showed weak correlations with leaf nutrient parameters (except for K). Precipitation and relative humidity, rather than temperature, showed significantly positive effects on leaf nutrients. These findings suggest that increasing water input and plant K content may be conducive to enhance the resistance and recovery ability of diseased wild apple trees.