Numerous studies have evaluated the composition of gut microbiota in experimental animals fed high-fat or low-fiber diets. However, few reports have focused on the effects of different fatty acid (FA) compositions on the diversity of gut microbiota and its metabolites. Therefore, the aim of this research was to investigate the effects of different dietary fats on liver mRNA expression levels of genes related to cholesterol and bile acid (BA) metabolism, as well as to investigate cecal microbiota composition and bacterial metabolites composition in rats. Four-week-old male Wistar/ST rats were fed a 15% fat diet for 30 days, including from different sources (soybean oil, lard, menhaden oil, or tuna oil). Then, the rats’ cecal microbiota composition was determined by sequencing the 16S ribosomal RNA gene using next-generation sequencing. Lard diet drastically decreased the expression level of liver ATP-binding cassette subfamily G genes (Abcg5 and Abcg8 genes) compared with other diets. Menhaden oil diet increased the fecal BA excretion compared with soybean oil and lard diets. Fecal BA excretion tended to be positively correlated with the relative abundance of Firmicutes, and negatively correlated with the relative abundance of Bacteroidetes. These results have shown that dietary fats with different FA compositions have a different effect on the relative composition of cecal microbiota, and in particular, menhaden oil may have very different effects compared to other experimental fats. The effects of fish oils on the cecal microbiota may differ greatly depending on the ratio of EPA to DHA and the composition of FA other than n-3 polyunsaturated FA. Our results provided new insights on the way different dietary fat sources affect sterol metabolism and alter cecal microbiota composition in rats.