Brassica chinensis L. is often grown using ‘excessive water and fertilizer’, which has a negative impact on the inter-root soil environment and the yield and quality of the plant. As the concept of green and sustainable development takes root in people’s minds, it is important to determine the right amount of water and fertilizer. Based on this, the effects of different irrigation rates and microbial fertilizers on the inter-root soil environment and yield and quality of B. chinensis were investigated. A pot experiment was carried out with two irrigation levels (W1: 80–90% of field water capacity; W2: 70–80% of field water capacity) and three fertilizer treatments (F0: no fertilizer; F1: CPS Powder Drill microbial fertilizers; F2: Maya 85 microbial fertilizers). The results showed that microbial fertilizer and irrigation amount, as well as their interaction, all had significant effects on yield, polyphenol content, soluble protein content, nitrate content, and the activities of soil enzymes, such as urease, sucrase, and catalase (p < 0.05). Increases in irrigation amount and the application of microbial fertilizer can increase the yield of B. chinensis, effectively improve the activities of sucrase, urease, and catalase in soil, increase the contents of vitamin C, chlorophyll, soluble protein, and total phenol in leaves, and reduce the content of nitrate. In addition, the findings of the principal component analysis indicated that the F2W2 treatment was the optimal treatment. The results of this study demonstrate that an 80–90% field water capacity, in conjunction with Maya 85 microbial fertilizers, yields an optimal outcome, with a score of 1.86. This outcome suggests that this combination of water and fertilizer can be used as a recommended protocol for the cultivation of Brassica chinensis L.