The knowledge-based phosphorus (P) input in farmlands is an approved management practice for enhancing soil P supply and crop production. To maintain crop production and ensure the efficient application of P resources, it is crucial to better understand the impacts of P inputs on agroecosystem production and functional services, as well as their relationships with soil biodiversity. A decade-long field experiment was established to explore the impacts of P fertilizer input levels on the multiple ecosystem functions (ecosystem multifunctionality, EMF) of paddy fields, with particular attention to link between soil biodiversity and the EMF. By integrating 22 single-ecosystem functions, our results suggested that P fertilizer inputs significantly increased the EMF and most single-ecosystem functions, which was related to certain characteristics, including crop productivity, soil carbon and nutrient storage, element cycles, and microbial growth. The soils with different P input levels exhibited different richness of fungi, bacteria and protists, with these diverse responses to the P fertilizer inputs being significantly different across rice three growth stages. Soil bacterial and fungal richness exhibited positive linear relationships with the EMF index and most the single-ecosystem functions during both early and late rice seasons. Among the microbial taxa, fungal richness was the key driver and predictor of the EMF, followed by bacterial richness. In addition, among soil nutrient properties, available P content was the dominant driver and predictor of the EMF, followed by NO3--N content. Phosphorus fertilizer input rate significantly influenced the link between soil microbial diversity and the EMF, with the P-input-driven impacts on this relationship being further regulated by soil available P and NO3--N contents. By linking the EMF with the species-rich soil microbial diversity, our results would provide in-depth insights into maintaining crop production and P efficient utilization, emphasizing the importance of understanding the co-regulation of fertilizer inputs on agroecosystem production and ecological service trade-off.