Wild soybeans, the ancestors of soybeans, are important genetic resources. Unfortunately, some natural populations of them are declining inexplicably. This study revealed the drivers behind this decline to inform conservation strategies. Conducted in the northeastern Inner Mongolia, China, the study analyzed 12 community characteristics across 20 herbaceous communities to gain insights into the causes and mechanisms of the decline. The wild soybean populations face at least three stress factors: external environments, internal community structures, and the planting industry, and these factors exhibit distinct stress mechanisms. The results mainly included that: 1. Two correlations as regulatory factors involved in maintaining community stabilizing, i.e., the CNDP effect (conspecific negative density-plant weight correlation, density effect) between density and single-plant weight of wild soybeans in the populations, and the HDC effect (heterospecific density complementary relation) between densities of both wild soybeans and other companion plants in the communities. 2. Shading stress reduced companion plant density but increased wild soybean density via the HDC effect and CNDP effect. 3. Stressed habitats favored perennial plants, significantly outnumbering annual ones. 4. Our results demonstrated that perennial herb density increases with latitude, while herbaceous communities exhibited a latitudinal diversity gradient (LDG), gradually decreasing in diversity with increasing latitude. 5. The intra-community structures with high perennial ratios threatened wild soybeans by favoring perennial dominance. 6. The wild soybean populations near cropland experienced a severe decline compared to those far from the cropland. Practical implication: This study demonstrates that community environments, high perennial species ratios, and the planting industry affect the survival of natural wild soybeans in agroecosystems. The high perennial species ratio serves as an important intra-community biological stressor, threatening annual wild soybeans, while herbicide spraying on croplands would reduce the individual density of natural wild soybean populations near croplands. The research results can be used to guide the protection of wild soybeans in the field and suggest that if wild soybean populations are to be maintained, then artificial intervention is necessary to control community succession of in-situ wild soybean nature reserves to prevent any plant from gaining ecological advantages for stable coexistence.