【Objective】 The global wolfberry(Lycium barbarum L.) industry is undergoing a paradigm shift from traditional Ningxia-dominated production to multipolar cultivation systems across Northwest China. In this transitional context, developing sustainable soil management strategies becomes imperative for maintaining agricultural productivity and ecosystem resilience. While cover crop intercropping has emerged as an advanced agroecological practice demonstrating dual benefits in fruit quality enhancement and environmental stewardship, conventional field management approaches; particularly long-term monoculture and chemical fertilizer overapplication, continue to compromise both yield and phytochemical quality of wolfberry. This study systematically investigates the rhizosphere engineering effects of wolfberry/forage radish (Raphanus sativus L.) intercropping coupled with organic fertilization, focusing on its mechanistic impacts on soil microbiome restructuring and metabolic reprogramming. 【Method】 This study investigated the effects of wolfberry (Lycium barbarum L.)/radish (Raphanus sativus L.) intercropping with manure on edaphic microbial communities and metabolite profiles through a split-plot field experiment (2019-2021) in arid northwestern China. It also considered the effects of cover crop planting patterns on soil microbial community structure, metabolite composition, and yield of wolfberry orchards. Three organic fertilization regimes(0, 6 660 kg·hm^-2, and 13 320 kg·hm^-2) were applied under two planting systems: monoculture (M) and intercropping(I). Using Illumina high-throughput sequencing technology, quantitative PCR methods, and liquid chromatography-tandem mass spectrometry (LC-MS), microbial information and metabolites were measured. The correlation between soil physicochemical properties, microbial diversity, key metabolite components, crop yield and its differential metabolites, microbial diversity index, and environmental factors under different planting modes was analyzed. 【Result】 Compared with the traditional wolfberry monoculture, intercropping significantly enhanced soil multifunctionality, increasing surface soil electrical conductivity(EC) by 29.66%, organic carbon (SOC) by 47.80%, total nitrogen (TN) by 39.09%, available nitrogen (AN) by 46.23%, available potassium (AK) by 36.64%, and microbial biomass nitrogen (MBN) by 22.56%compared with monoculture (P<0.05). Additionally, intercropping enhanced soil microbial diversity, with the bacterial Shannon index increasing by 4%and the Simpson index decreasing by 43.04%. Metabolomic analysis identified 867 metabolites, including 84 differentially abundant compounds such as lipids, organic acids, phenylpropanoids, and carbohydrates. Among these, two key metabolites were positively correlated with yield enhancement. Consequently, wolfberry yield increased significantly by 6.36%. 【Conclusion】 These findings indicated that cover crop intercropping improved soil microecological conditions, induced specific metabolite shifts, and effectively enhanced wolfberry productivity, demonstrating its applicability in sustainable wolfberry cultivation systems.