Obesity has become a global public health problem, and its relationship with gastrointestinal diseases has become a major concern. The visceral adiposity index (VAI) is a novel index to assess the distribution and content of visceral fat, and this study aimed to investigate the association between VAI and bowel habits (chronic diarrhea, chronic constipation) and inflammatory bowel disease (IBD). The 2005-2010 National Health and Nutrition Examination Survey (NHANES) dataset was used for the cross-sectional survey. Bowel habits and IBD were defined by self-report. Multiple logistic regression models were used to test the linear association of VAI with bowel habits and IBD. Fitted smoothed curves and threshold effects analyses were used to characterize nonlinear relationships. This cross-sectional study included 10,391 adults (≥ 20 years). After adjusting for covariates, there was a significant negative association between VAI and chronic constipation (OR [95% CI]: 0.97 [0.95, 1.00]) but no significant association with IBD (OR [95% CI]: 0.97 [0.87, 1.07]). Additionally, there was a nonlinear association between VAI and chronic diarrhea with a breakpoint of 3.08, with a positive correlation between the two on the left side of the breakpoint and no statistical significance on the right side. Subgroup analyses and interaction tests showed that maintaining sleep health was associated with a low risk of chronic constipation. Elevated VAI levels were negatively associated with chronic constipation, and elevated levels were positively associated with chronic diarrhea at VAI < 3.08. This reminds us that maintaining moderate levels of visceral fat may prevent the onset of chronic constipation and circumvent the risk of chronic diarrhea. Notably, maintaining healthy sleep may play a positive role in reducing chronic constipation.