This study aimed to elucidate the biological mechanisms through which different tillage practices affect wheat yield and nutrient use efficiency under straw return conditions, focusing on rhizosphere microbial communities, metabolite profiles, and their interactions to inform improved agricultural management. The field experiment tested three treatments: no-tillage with all straw mulching (SN), rotary tillage straw return (SR), and plow tillage straw return (SP). Using high-throughput sequencing and liquid chromatography-tandem mass spectrometry, we investigated how different treatments affected the microbial community in wheat rhizosphere soil and metabolic functions through microbiome and non-targeted metabolomics analyses. SN helped to increase the wheat yield, soil nutrient content in the plow layer, and enzyme activity. Compared with SN, the yields were 8.3% and 12.4% lower under SR and SP, respectively, the soil organic carbon contents were 13.2% and 5.6% lower, and the pH values were 2.7% and 1.2% higher. Tillage practices significantly altered the composition and diversity of the bacterial and fungal communities. The species richness of bacterial and fungal communities followed the order of: SP > SR > SN and SN > SP > SR, respectively. The stabilities of the bacterial and fungal communities exhibited the same distribution pattern. Principal coordinate analysis and PERMANOVA indicated that under straw return, different tillage practices led to significant separation of soil bacterial and fungal communities. Furthermore, Actinobacteria and Proteobacteria contributed most significantly to differences in the bacterial community structures, and Ascomycota and Basidiomycota contributed most significantly to differences in the fungal community structures. Under straw return, different tillage practices significantly altered soil metabolite composition. Bacterial communities correlated more strongly with soil metabolites than fungal communities. Compared with SN, metabolic pathways for different metabolites were enriched under SR and SP, and all were related to amino acid metabolism, putatively mainly in the valine, leucine, and isoleucine biosynthesis pathways. Collectively, our findings demonstrate that tillage practice is a key regulator of straw-amended soil ecosystems, and that no-till with straw mulching optimizes yield and nutrient efficiency primarily by enhancing the functional synergy between the rhizosphere microbiome and metabolome.