Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in the arid regions of Northwest China, yet its straw resources remain underutilized. This study investigated the effects of applying fermented J. artichoke straw at different rates (0%, 20%, 40%, and 60%) on chili pepper growth and soil health in long-term continuous cropping systems. The results demonstrated that straw application generally enhanced dry matter accumulation and yield per plant, with the 20% - 40% treatments showing the most favorable effects and significantly promoting root growth (P < 0.05). In terms of soil properties, the 20% - 40% treatments significantly improved soil nutrient status, while the 40% treatment notably enhanced soil enzyme activity. The 60% treatment significantly reduced alkali hydrolyzable nitrogen, available potassium content, and urease activity, but markedly increased total and available phosphorus levels. All straw applications significantly lowered soil pH. Microbial community analysis revealed that straw addition increased bacterial diversity and richness, with the 20% - 40% treatments significantly enriching beneficial taxa such as g_Sphingomonas, g_Bacillus, and g_Lysobacter. Metabolomic analysis identified sucrose and derivatives, and 1-Hexacosanol as key response metabolites, whose variations were closely correlated with microbial community structure and plant growth improvement. This study clarifies the critical role of fermented J. artichoke straw application rates in regulating rhizosphere microecology, providing a theoretical foundation for mitigating continuous cropping obstacles and promoting straw resource utilization.