The aim of this study was to investigate the effect of low-dose CT enterography (CTE) based on modified guided image filtering (GIF) algorithm in the differential diagnosis of ulcerative colitis (UC) and Crohn’s disease (CD). Methods. One hundred and twenty patients with suspected diagnosis of IBD were studied. They were randomly divided into control group (routine CT examination) and observation group (low-dose CTE examination based on improved GIF algorithm), with 60 cases in each group. Comprehensive diagnosis was used as the standard to assess the diagnostic effect. Results. (1) The peak signal-to-noise ratio (PSNR) (26.02 dB) and structural similarity (SSIM) (0.8921) of the algorithm were higher than those of GIF (17.22 dB/0.8491), weighted guided image filtering (WGIF) (23.78 dB/0.8489), and gradient domain guided image filtering (GGIF) (23.77 dB/0.7567) ( P < 0.05 ); (2) the diagnostic sensitivity (91.49%), specificity (92.31%), accuracy (91.67%), positive predictive value (97.73%), and negative predictive value (75%) of the observation group were higher than those of the control group ( P < 0.05 ); the sensitivity and specificity of CTE in the diagnosis of UD and CD were 96.77% and 81.25% and 98.33% and 93.33%, respectively ( P < 0.05 ); there were significant differences in symmetrical intestinal wall thickening and smooth serosal surface between UD and CD ( P < 0.05 ). Conclusion. (1) The improved GIF algorithm has a more effective application value in the denoising processing of low-dose CT images and can better improve the image quality; (2) the accuracy of CTE in the diagnosis of IBD is high, and CTE is of great value in the differential diagnosis of UD and CD.