Objective Ankylosing spondylitis sacroiliac joint disease using MRI and CT diagnosis in two different ways, the clinical value comparison of two diagnostic methods, that the clinical diagnosis and treatment options provide a strong reference. Methods Select this institute admitted 78 cases of patients with ankylosing spondylitis as the object of this study, and were used MRI and CT examination of the patient, but to judge and compare the clinical lesions examined in accordance with this outcome. Observed two groups of patients clinically diagnosed cases and compared between the two bone abnormalities detected by those who, to be analyzed. Results The inspection found that, MRI detected bone abnormalities was significantly lower than CT detection rate (P<0.05). However, CT examination stage I disease ankylosing spondylitis sacroiliac sensitivity of 17.95% (14/78) was significantly lower than the sensitivity of MRI examination was 33.33% (26/78) (P<0.05); and for detecting lesions above the level II the case, two were not statistically significant (P>0.05). Conclusion Compared to MRI diagnosis, the clinical use of CT scanning in the diagnosis of ankylosing spondylitis sacroiliac joint disease has a higher spatial resolution, it can effectively improve the clinical diagnosis rate, thus better for the clinical judgment of ankylosing sacroiliac joint lesions provide a reference value. However, the clinical use of MRI for the diagnosis of ankylosing sacroiliac joint disease, it may be better to be fat deposition in patients with articular cartilage lesions clear display, which found in favor of minor illness. Therefore, MRI examination is generally used to detect early ankylosing spondylitis sacroiliac joint disease.