【Objective】This study aimed to examine the impacts of microbial diversity loss on paddy soil multifunctionality, and elucidate the regulatory roles of abundant, moderate, and rare microbial taxa. 【Method】Microbial diversity gradients (D0, D1, D3, D6) were established via the dilution-to-extinction approach and functional genes involved in C, N, P, and S cycling in topsoil (0-20 cm) and subsoil (40-60 cm) of a paddy field were quantified using high-throughput qPCR. Soil multifunctionality was assessed using both the averaging and multi-threshold methods. High-throughput sequencing was employed to analyze the diversity, community structure, and co-occurrence network properties of the three microbial taxa and their relationships with soil multifunctionality. 【Result】Results showed that the responses of soil multifunctionality in topsoil and subsoil to microbial diversity loss were different. Compared with the original soil (D0), the averaging method indicated that different dilution levels (D1, D3, D6) significantly reduced topsoil multifunctionality. The reduction rates were 75.8%-85.8%, 74.6%-80.0%, and 59.8%-64.8% under the rice-fallow (RF), rice-wheat (RW), and rice-milk vetch (RM) cropping systems, respectively, with no significant differences among the dilution levels. In contrast, although subsoil multifunctionality showed minor fluctuations (ranging from 0.05 to 0.28), no significant differences were observed between different dilution levels and the original soil except for the D3 treatment under the RM cropping system. This pattern was further verified by the multi-threshold method. Although the diversity of all three taxa significantly decreased with increasing dilution, the community structure of rare taxa remained relatively stable. Co-occurrence network analysis revealed that topological properties (degree, clustering coefficient) of all three taxa decreased significantly in topsoil under dilution. In contrast, rare taxa in subsoil maintained stable network properties despite dilution. Correlation analysis further indicated that topsoil multifunctionality was closely linked to the diversity, composition, and network topology of all three microbial taxa, while subsoil multifunctionality was primarily associated with the degree and clustering coefficient of rare taxa, which underscores the key role of rare taxa in sustaining subsoil multifunctionality in the face of microbial diversity loss. 【Conclusion】Microbial diversity loss induces differential responses of soil multifunctionality in topsoil and subsoil, which is closely related to the diversity, community structure, and co-occurrence networks of microbial subcommunities in different soil layers.