Magnetic nanoparticle-mediated isolation (MMI) method is a promising technology for separating functional microbes from complex microbiota. In this study, we employed the MMI method to recover metabolically active cellulose decomposers from paddy soils with a 28-year history of different fertilization regimes (chemical fertilizers; termed NPK afterwards), organic amendments (OM), and without fertilization (CK)). Our findings suggest that compared to no fertilization, fertilization increased the number and activity of microorganisms, thereby facilitating cellulose degradation. These active cellulose-degrading bacterial phylotypes mainly belong to Bacteroides and Firmicutes at the phylum level, and further to Porphyromonadaceae and Paenibacillaceae at the family level. Also, we found that fertilization increased community stability, partly by decreasing interspecies dependency. Furthermore, OM fertilization increased the numbers of potential ecological function，which makes it more effective than NPK fertilization. These results were consistent with our previous conclusions based on DNA-SIP technology, suggesting that MMI is a powerful approach to recover active cellulose decomposers from a complex microbial community. Above all, these results would deepen our understanding of keystone straw decomposers in paddy soils and their shifts in response to different fertilizations.