Anal fistula (AF) is an abnormal tunnel under the skin connecting the anal canal in the colon to the skin of buttocks. Fat-suppressed (FS) proton density-weighted (PDW) imaging is mainly used for the diagnosis of diseases involving bones and joints. Until now, its value in the diagnosis of anal fistula has been rarely reported. To compare three magnetic resonance imaging (MRI) sequences - diffusion-weighted imaging (DWI), FS-PDW), and contrast-enhanced (CE) T1-weighted (T1W) imaging - for the diagnostic value of the internal opening of AF. MRI scans of 132 patients suspected of having AF between December 2021 and April 2023 were retrospectively analyzed. In total, 65 patients who underwent preoperative MRI and were treated surgically were included. The lesion conspicuity and accuracy for featuring AF were calculated by evaluating the three imaging datasets DWI, FS-PDW, and CE-T1W imaging, with surgical findings serving as the reference standard for the presence of fistulas. The statistical analysis included the application of the chi-square test and Kruskal-Wallis test. In 65 patients with AF, 87 internal openings of AF were confirmed. In terms of the diagnostic accuracy of the internal openings, both FS-PDW and CE-T1W imaging sequences were significantly better than DWI sequences, and the difference was statistically significant (P < 0.05). The FS-PDW imaging sequence showed comparable diagnostic performance of the internal opening of AF to CE-T1W imaging, which can provide an important diagnostic basis for clinical procedures.