［Objective］This study aimed to investigate the effects of water-fertilizer management and greenhouse intercropping on soil microecology and the quality of cucumber and celery.［Methods］ A three-year field experiment was conducted. Two water-fertilizer modes，including continuous fertilization in irrigation（CF）and alternating fertilization in irrigation （AF），were employed. There were three planting patterns，including cucumber monoculture（CU），celery monoculture（CE），and cucumber-celery intercropping（CC）. The impacts of different treatments on crop quality， soil physicochemical properties， and microbial communities were systematically evaluated.［Results］The CCCF treatment significantly enhanced the vitamin C content in both cucumber and celery（16.6%-200%），while the CUCF treatment exhibited advantages in soluble sugar accumulation. XGB model analysis revealed that available potassium and pH were the key factors regulating vitamin C and soluble sugar content，respectively. Microbiome analysis indicated that intercropping treatments enriched specific ASVs（7 371-7 526）and significantly increased the abundance of plant growth-promoting bacteria，including Steroidobacter and Flavobacterium，while inhibiting pathogenic fungal growth. Functional prediction showed that water-fertilizer management primarily influenced nitrogen cycling functions，whereas intercropping enhanced methanotrophy functions. Microbial co-occurrence network analysis further revealed that CF formed tight bacterial networks，AF increased network modularity，and CC maintained high connectivity while preserving moderate modularity.［Conclusion］Different water-fertilizer and planting management practices differentially influenced crop quality through the regulation of soil physicochemical properties， microbial community structure，and ecological networks. Specifically，CCCF and CUCF were suitable for enhancing vitamin C and soluble sugar content，respectively，providing new insights for precise quality regulation in protected agriculture.