In order to investigate the causes of degradation and the difficult problems in seedlings breeding of Amygdalus mongolica, the response characteristics of the seed germination and seedling growth of Amygdalus mongolica to adverse ecological factors were investigated, using a method of indoor control of drought stress, mixed salt stress, variable temperatures and seed husking, with the seeds of A. mongolica in the middle section of the Qilian Mountain. The results showed insignificant difference in the germination rate (P>0.05) of the A. mongolica seeds processed in clean water for control and -0.15 MPa PEG solution, and significant sequential decrease in the germination rate (P<0.01) processed in the water potentials of -0.32, -0.54, and -0.81 MPa, and non-germination processed in -1.15 MPa, and non-germination processed in -1.15 MPa. As the drought worsened and water potential decreased, the germination was delayed, the germination and vitality indices, the primary bud rates, root lengths, number of secondary roots and fresh weights of seedlings were on a significantly decreasing trend (P<0.01). But the sound seedling index were significantly increased in case of treatment in -0.32 MPa. And the lowest thresholds of osmotic potential for seed germination was -0.81 MPa. The lowest mixed salt stress threshold for seed germination was 1.6%. Under light mixed salt stress (0.2%-0.4%), the length of primary buds and the number of secondary roots increased. With the increase in the mixed salt stress, the dry weight of primary buds and the fresh weight of seedlings were decreased, indicating that the seedlings responded and adapted to light mixed salt stress by reducing growth to promote root growth. After the stress of low osmotic potential or high-concentration mixed salt, a certain amount of the seeds developed into dormancy to maintain life force. The ungerminated seeds showed a germination rate of 62%-96% after rewatering, and the total of the primary germination rate and the re-germination rate was not different from the germination rate of the control seeds (P>0.05). The obstacle of seed coat is the main factor restricting seed germination. Seed dormancy can be interrupted by mechanical peeling. Stratification of seeds in low temperature (2-5℃) can significantly enhance seed vitality, and stratification in variable temperatures (5-10℃) can significantly improve the germination rate and vigor. The causes of degradation of A. mongolica include low water potential, high salt stress, high temperature, sensitive dormancy of seeds, and poor cold resistance of seedlings. For saving and manual breeding of A. mongolica, an area with irrigation conditions and of low temperature in spring should be selected for raising of seedlings, and sowing of seeds is suggested to occur at the time of soil thawing, to take advantage of the low temperature in early spring to and wake the seeds from their dormancy and cultivate strong seedlings.