The present study investigated the effects of CS@Fe3O4 nanoparticles combined with microwave or far infrared thawing on microbial diversity of red seabream (Pagrus major) fillets in terms of thawing loss, pH, TVB-N, classical microbiological enumeration and high-throughput sequencing, and the same parameters were also studied for 24 h after thawing. Four thawing methods were used: microwave thawing (MT), far-infrared thawing (FT), CS@Fe3O4 nanoparticles combined with microwave thawing (CMT) and CS@Fe3O4 nanoparticles combined with far-infrared thawing (CFT). The results showed that CFT and CMT had lower values of pH and TVB-N compared to the FT and MT. Based on conventional microbial count analysis, CFT and CMT samples also maintained lower TVC, pseudomonas and LAB counts. Using high-throughput sequencing analysis, Compared with FT and MT, CFT and CMT samples showed a significant decrease in the proportion of the Pseudomonadaceae flora. However, the proportion of Pseudomonas, Bacillaceae and Thermaceae also increased significantly after 24 h of storage, which indicated that become the predominant microbiota in red seabream (Pagrus major) fillets.