[Objectives] The Alligator sinensis, classified as a national first-class key protected wild animal, has consistently been a concern for conservationists regarding the improvement of artificial breeding and management standards. This study aims to explore the optimization of feeding patterns for A. sinensis. [Methods] The experiment utilized four different types of feeding:Feeding Group 1 (traditional frozen animal-derived feed), Feeding Group 2 (mixed pellet feed), Feeding Group 3 (mixed pellet feed with chelated sodium butyrate) and Feeding Group 4 (mixed pellet feed with complex Bacillus spores). By collecting feces from each feeding group and analyzing the changes in gut microbiota using 16S rDNA amplicon sequencing, combined with comparative analysis of data such as average clutch size, fertilization rate, and hatching rate of fertilized eggs during the breeding season, the study comprehensively evaluated the impact of different types of feeding on the diversity of gut microbial communities and reproductive performance in A. sinensis. Statistical analysis and data processing were performed using Excel 2010 and SPSS version 26.0. [Results] In terms of intestinal microbial richness and diversity, the intestinal flora of Feeding Group 1 exhibited the highest richness, while Feeding Group 4 had the highest diversity (Table 1). No significant differences were observed in the dominant flora at the phylum level (Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota) among the different feeding groups of experimental crocodiles. At the genus level, the microbial abundance of Brevibacillus, Cetobacterium, and Paenibacillus in Feeding Group 2, Cetobacterium, Kurthia, and Sphingobacterium in Feeding Group 3, and Brevibacillus, Paenibacillus, and Glutamicibacter in Feeding Group 4 were significantly higher than those in Feeding Group 1 (Fig. 3). The PICRUSt2 functional enrichment analysis revealed that the intestinal flora of Feeding Groups 2 and 4 exhibited the highest relative abundance across fourteen functions, including cell motility, signal transduction, transcription, and amino acid metabolism (Fig. 5). A comparison of the annual egg-laying performance of the four feeding groups of A. sinensis revealed that the numbers of egg-laying nests in Feeding Group 2 (5 nests), Feeding Group 3 (1 nest), and Feeding Group 4 (1 nest) were higher than that in Feeding Group 1 (0 nest). The number of eggs per nest and fertilization rate for Feeding Group 3 were 31 eggs and 91.2%, for Feeding Group 4 were 29 eggs and 89.5%, and the mean number of eggs per nest for Feeding Group 2 were 28.6 ± 4.5 eggs and 85.6% ± 2.3%. After excluding unfertilized eggs, the hatching rate for Feeding Group 4 was 95.9%, for Feeding Group 3 was 92.5%, and the average hatching rate for Feeding Group 2 was 95.3% ± 2.8% (Table 2). [Conclusion] In summary, the mixed particle feed has a positive impact on the intestinal flora structure of A. sinensis, optimizing the composition of intestinal microbes and enhancing the reproductive performance of A. sinensis. This provides a novel approach to the artificial breeding management of A. sinensis, which has the potential to enhance breeding outcomes and the quality of life of A. sinensis.