Observational studies highlighted an association between the appendix and inflammatory bowel disease (IBD). However, it's unclear whether the identified association is causal because of difficulties in establishing a clear temporal sequence. We investigated the association between acute appendicitis, appendectomy, and IBD by using two-sample bidirectional univariable Mendelian randomization (UVMR), multivariable MR (MVMR) and linkage disequilibrium score regression (LDSC) analyses. Eligible instrumental variables were screened from previous genome-wide association studies (GWAS) of European ancestry for analysis. The inverse variance-weighted (IVW) method was used for the primary analysis. Sensitivity analyses were used to detect and correct pleiotropy. LDSC analysis determined SNP-based heritability (h2) for acute appendicitis, IBD, Crohn's disease (CD), and ulcerative colitis (UC). Following that, cross-trait LDSC analysis assessed genetic correlations (rg) between these traits using GWAS summary data. Genetically predicted UC was associated with a significantly lower risk of acute appendicitis (OR = 0.933, P < 0.001) and appendectomy (OR = 0.954, P < 0.001), but conversely, acute appendicitis or appendectomy had no causal effect on IBD, UC or CD (all P > 0.05). CD had a suggestive association with appendectomy (OR = 0.981, P = 0.018) but was not significant after excluding the effect of UC by MVMR (OR = 0.999, P = 0.889). Furthermore, LDSC suggested a negative genetic correlation between UC and acute appendicitis (rg = -0.205, P = 0.005). In conclusion, our study confirms UC casually leads to a decreased risk of acute appendicitis and appendectomy, but neither acute appendicitis nor appendectomy reduces the risk of IBD, UC, and CD.