In recent years, the theory of biological diversity and stability has become one of the hotspots in river ecology. To explore the distribution patterns of benthic invertebrate diversity and community stability, and identify their driving factors, a field investigation based on environmental DNA technology (eDNA) was conducted during August 2021 at 10 sampling sites in a mountainous river of Jinan section at lower Yellow River Basin. According to land-use types, the study area was divided into three categories: low disturbance zone (Low), moderate disturbance zone (Moderate), and high disturbance zone (High). Then, we analyzed the distribution patterns of environmental factors, benthic invertebrate diversity and community stability at the three disturbance zones, and simultaneously identified their driving factors. Results showed that: ① The environmental factors, including electrical conductivity (EC), total nitrogen (TN) and nitrate nitrogen (NO^-₃-N), exhibited a trend of high disturbance zone > moderate disturbance zone > low disturbance zone. Concentrations of these environmental factors were (569.33±37.44) μS/cm, (6.73±1.20) mg/L and (6.17±1.15) mg/L at high disturbance zone, (554.75±47.58) μS/cm, (4.05±0.63) mg/L and (2.84±0.68) mg/L at moderate disturbance zone, and (359.67±34.07) μS/cm, (3.02±0.52) mg/L and (2.43±0.58) at low disturbance zone, respectively. ② Biodiversity indices, such as Margalef abundance index (d), Pielou evenness index (J), community stability index (ICV), and cohesion index (|Negative cohesion|/Positive cohesion) showed the highest values at moderate disturbance zone with average±standard error of 3.75±0.07, 0.76±0.02, 1.90±0.11 and 1.45±0.27, respectively. ③ Ammonia nitrogen (NH₃-N) and community composition change had positive effect on Margalef abundance index (d) (r=0.52, P < 0.05) and the species richness S of benthic invertebrate (r=0.67, P < 0.05), respectively. ④ Analysis of structural equation model (SEM) revealed that EC, NH₃-N and NO^-₃-N were the critical environmental stressors, and S and d were the primary biotic factors affecting the community stability (i.e., ICV and |Negative cohesion|/Positive cohesion) of benthic invertebrates. Among these factors, EC, NH₃-N and d were conducive to the construction of a stable mechanism for benthic invertebrate community with effect size of 0.43, 0.07 and 0.53 for ICV, and 0.06, 0.39 and 0.92 for |Negative cohesion|/Positive cohesion, respectively. Although high concentrations of NO^-₃-N and low species richness (S) significantly reduced the community stability, they promoted the relationships of species competition within the community. Overall, our study deeply revealed the mechanism of biotic and abiotic factors on the benthic invertebrate diversity and community stability in mountainous rivers, which provided a scientific basis for future ecosystem health management of mountainous rivers.