Objective Fecal microbiota transplantation (FMT) is a promising, but immature intervention in the current pig production. The aim of this study was to investigate the effects of aerobic and anaerobic FMT preparation (T1 group and T2 group, respectively) on fecal microbiota and metabolite profiles of SPF Bama mini pigs. Methods Amplicon sequencing and untargeted metabolomics method were used to reveal the effects of aerobic and anaerobic FMT preparation (T1 group and T2 group, respectively) on fecal microbiota and metabolite profiles of SPF Bama mini pigs. Results (1) The two FMT preparation method preserved all the bacterial phyla in untreated pig slurries ( C group). Firmicutes and Bacteroidetes constituted the top two phyla in the gut microbiota in all groups, and FMT preparation result ed in a significant decrease of Treponema bacteria. (2) In untreated pig slurries, the two most abundant fungal phyla were Ascomycota and Basidionmycota. FMT preparation significantly increased the relative abundance of Ascomycota, and aerobic FMT preparation removed the Wallemia genus. These changes in microbial community did not affect the functional contributions.(3) A total of 402 and 195 characteristic metabolites were respectively detected by positive and negative mode liquid chromatograohy-mass spectrometry, including Lipids and lipid molecules, and Organoheterocyclic compounds. Disturbance of amino acid metabolism, and lipid metabolism were the most significant in T1 versus C comparison, and T2 versus C comparison, 155 and 201 confirmed differential metabolites using reference compounds were identified, respectively. Highly positive correlated metabolites with Spearman correlation coefficient r> 0. 6 are connected with Trepronema_2 in T1 versus C and T2 versus C comparisons, and highly negative correlated metabolites with r< - 0. 4 are connected with Ruminococcaceae_ NK4A214 group in T1 versus C and T2 versus C comparisons. Conclusions Although the FMT preparation time is short, the effect of short aerobic exposure on the abundance of fungal communities in the samples was higher than that of short anaerobic exposure, and the relative abundance of harmful bacteria such as Treponema and Spirochaetes and related metabolites were effectively reduced, which could improve the safety of FMT.