This study aimed to investigate the association between the polymorphisms of the FUT2 gene (rs1047781, rs601338) and the FUT3 gene (rs3745635, rs28362459) with susceptibility to inflammatory bowel disease (IBD) in the Zhuang population of Guangxi. Intestinal mucosal tissues were collected from 113 Zhuang patients (41 with Crohn's disease [CD] and 72 with ulcerative colitis [UC]) and 120 han patients (42 with CD and 78 with UC), all of whom were unrelated and diagnosed with IBD, as well as from 106 Zhuang and 119 han unrelated healthy controls, from January 2021 to December 2023. DNA was extracted from intestinal mucosal samples in each group. FUT2 gene polymorphisms (rs1047781, rs601338) and FUT3 gene polymorphisms (rs3745635, rs28362459) were amplified using polymerase chain reaction (PCR). PCR product fragments were analyzed by DNA sequencing, and sequence analysis was conducted using the GenBank database. The genotype and allele frequencies of the FUT2 rs1047781 polymorphism in the Zhuang UC patient group were significantly different from those in the control group (P < 0.05). Similarly, significant differences were observed in the genotype and allele frequencies of the FUT3 rs3745635 polymorphism in the Zhuang UC and CD patient groups compared to controls (P < 0.05). No statistically significant differences were found in the genotype and allele frequencies of FUT2 rs1047781 between the Zhuang CD patients and controls (P > 0.05). Additionally, no significant differences were observed in the genotype and allele frequencies of FUT2 rs601338 and FUT3 rs28362459 polymorphisms between the Zhuang UC and CD patient groups and the controls (P > 0.05). The FUT2 rs1047781 and FUT3 rs3745635 polymorphisms may be associated with IBD in the Guangxi Zhuang population, while FUT2 rs601338 and FUT3 rs28362459 polymorphisms may not show such an association.