This study aimed to screen out the shrub species which can promote the seed germination and seedling growth of Amygdalus pedunculata Pall. and offer insight for ecological environment governance of the coal mines subsidence area in Mu Us Sandy Land, Yulin City of Shaanxi Province. The indoor bioassay method was used to study the aqueous leaf extracts from Amorpha fruticosa Linn., Hedysarum mongolicum Turez., Sabina vulgaris Ant., and Hippophae rhamnoides Linn. under different concentration gradients to examine seed germination, initial growth, and physiological and biochemical of two Amygdalus pedunculata varieties (YY-1 from Yuyang County (YY) and SM-6 from Shenmu County (SM), Shaanxi Province, China). The results showed that with aqueous leaf extracts concentrations at lower concentrations of 0.025 (T1) and 0.05 g·mL−1 (T2) from A. fruticosa, H. mongolicum, and S. vulgaris significantly promoted seed germination and seedling growth of two A. pedunculata varieties. Moreover, H. rhamnoides aqueous leaf extracts had the strongest inhibitory effect on seed germination and seedling growth of A. pedunculata, and death occurred at concentrations of 0.15 (T4) and 0.20 g·mL−1 (T5). The enzyme activity and chlorophyll content of the A. pedunculata leaves decreased with an increase in the aqueous leaf extracts concentration of the four shrubs; the change trend of malondialdehyde content was the opposite. Root activity of the A. pedunculata increased and then decreased. The H. mongolicum and S. vulgaris are the most suitable mixed tree species for YY-1, while H. mongolicum and A. fruticosa are the most suitable mixed tree species for SM-6 at a relatively low density with more security. The results provide a theoretical basis and technical support for the establishment of an artificial mixed forest of A. pedunculata in the coal mine subsidence area of Mu Us Sandy Land.