Changes in the physical structure and nutrients contents of apple branches were explored after decomposition, and the soil quality of an orchard was evaluated after returning apple branches in situ. Scanning electron microscopy, X-ray diffractometry, and Fourier transform infrared spectroscopy were used to analyse the structural changes of the experimental material. The results showed that the structure of this material is obviously destroyed in the transverse sections and longitudinal sections. Collapsed cell walls had a negative effect on complete branches, which presented sharp decreases in cellulose contents and the partial removal of lignin and carbohydrate contents by the third year. In a final analysis of the nutrients in the branches, there was an obvious decline in macroelements (e.g., phosphorus and potassium), whereas manganese, which is a limiting factor, increased by 4-fold compared with the control. The results indicated that the addition of mulch from branches can be used to maintain a high soil quality in the third year of decomposition.