<p>The significant economic burden of colorectal cancer (CRC) necessitates the development of innovative therapeutic approaches. Interest in the gut microbiota’s role in CRC has increased. Capecitabine, as a chemotherapy, may disrupt the balance of the intestinal microbiota. This study investigated the anticancer effects of capecitabine combined with fecal microbiota transplantation (FMT) in a CRC mouse model caused by azoxymethane and dextran sodium sulfate. FMT was achieved with fecal microbiota from healthy mice through enema. Capecitabine decreased the number and diameter of cancer foci in CRC mice, while FMT supplementation had a more noticeable impact, indicated by increased body weight and survival rate. Capecitabine significantly reduced the abundance of pathogenic bacteria in mice with CRC, such as <i>Bacteroides</i>, <i>Enterorhabdus</i>, <i>Monoglobus</i>, <i>Rodentibacter</i>, uncultured_rumen_bacterium, <i>Turicibacter</i>, and <i>Streptococcus</i>. The supplementation of FMT more effectively reversed the gut microbiota dysbiosis in CRC mice, as demonstrated by the ACE and Chao 1 indices, PCoA analysis, and enhanced normal biological pathways. Microbial dysbiosis induced immunological dysfunction in CRC mice, indicated by abnormal immune cell recruitment and excessive cytokine production. Capecitabine treatment reduced immune cell infiltration, including CD3⁺ T cells, CD4⁺ T cells, and CD49b⁺ NK cells, as chemotherapy often suppresses the immune system. The supplement of FMT increased the proportion of CD4⁺ T cells, CD49b⁺ NK cells, CD8⁺ T cells, and LY6G⁺ neutrophils, indicating improved immune responses against CRC. Moreover, capecitabine therapy alone reduced the overexpression of IL1a, IL6, IL12a, IL12b, IL17, IL22, FOXP3, STAT3, IFN-γ, TNF-α, TGF-β, GZMA, CXCR4, OPN, PD-1 and PD-L1. FMT supplementation resulted in a higher immune response to CRC, as it had a greater inhibitory effect on the overexpression of inflammatory cytokines and enhanced the production of IL10, IFN-γ, and CXCR4. These cytokines were positively correlated with <i>Azospirillum_sp._47_25</i>, <i>Romboutsia</i>, <i>Lactococcus</i>, Rikenella_sp._Marseille_P3215 and <i>Turicibacter</i> and negatively correlated with <i>Parabacteroids</i>, unclassified_Oscillospiraceae, <i>Marvinbryantia</i>, unclassified_Clostridia_vadinBB60_group, unclassified_Erysipelatoclostridiaceae, <i>A2</i>, <i>Roseburia</i>, Rikenellaceae_RC9_gut_group, <i>Acetatifactor</i> and unclassified_Clostridia. The combination of capecitabine and FMT is more effective at preventing CRC than capecitabine alone, as it reverses gut microbial abnormalities and boosts immune responses to CRC.</p>