The reasons for the rapid degradation of the Betula microphylla population in the mushroom lake wetland on the southern margin of the Junggar Basin remain unclear. To investigate the various factors of the degradation, plant diversity and related indices were calculated based on data. Relationships of stoichiometric characteristics between plant leaves and soils were presented through correlation analysis, genetic differences were then analysed across the SLAF-seq technology. The results showed that (1) there were only 132 live plants, a decrease of 86.34% compared with 2013, and 75.91% of the dead plants, indicated that the population was extremely damaged. (2) In terms of plant community composition, compared with 2013, there were 119 species in 80 genera and 36 families, but now there are only 47 species in 40 genera and 23 families. Shannon diversity index of the community decreased from 1.5 to 1.14, followed by Pielous index from 0.21 to 0.16. The drop of plant diversity and Evenness index indirectly damaged root protection barrier and its ability to resist extreme weather began to decline. (3) The average soil pH value was 6.98, neutral soil; average contents of total nitrogen, total phosphorus and total potassium were 125.08 g/kg, 13.25 g/kg, and 9.16 g/kg, respectively, and the soil fertility could meet the growth needs of B. microphylla; The soil water content was 21.39%, which was significantly lower than the Ebinur Lake B. microphylla population (48.44%); The decrease of soil water content weakened the seedling regeneration mechanism, which was also one of the main factors leading to the degradation of this population. (4) Human disturbance and natural disaster factors could not be ignored in the formation and development of wild minimal populations. (5) The heterozygosity of the SNP (single nucleotide polymorphism) sites in this population was higher, SNP polymorphism and integrity was lower than Ebinur Lake Reserve population, and the phenomenon of genetic decline due to habitat degradation had been shown. In conclusion, the rapid degradation of the B. microphylla population was caused by many factors. It was urgent for the competent authorities to take actions and avoid the risk of extinction. Our research will provide a scientific basis for vegetation restoration and conservation in this area.