Purpose The recently available gated T1-weighted imaging with the Dixon technique enables the synchronized gating signal for both MR acquisition and PET reconstruction. Herein, we evaluated the clinical value of this MR-gated PET reconstruction in the thoracic-abdominal PET/MRI compared with non-MR-gated method. Methods Twenty patients (28 hypermetabolic target lesions) underwent PET/MRI. Four types of PET images were reconstructed: non-MR-gating + gated attenuation correction (AC) (group A), MR-gating + gated AC (group B), non-MR-gating + breath-hold (BH) AC (group C), and MR-gating + BH AC (group D). A 4-point objective scale (from well match to obvious mismatch was scored from 3 to 0) was proposed to evaluate the mismatch. The detection rate and quantitative metrics were also evaluated. Results In the patient-based analysis, for groups A through D, the detection rates were 90%, 100%, 85%, and 90% as well as 95%, 100%, 85%, and 85%, assessed by readers 1 and 2, respectively, and significant difference of mismatch score was observed with the highest proportion of 3 points in group B (85%, 90%, 35%, and 40%, and 80%, 90%, 35%, and 20%, assessed by readers 1 and 2, respectively). The lesion-based analysis demonstrated significant differences in quantitative metrics for groups A through D (all P's < 0.05), with the highest quantitative metrics in group B (SUVmax: 7.49 +/- 3.37, 8.45 +/- 3.82, 6.90 +/- 3.24, and 7.69 +/- 3.50; SUVmean: 3.90 +/- 1.60, 4.34 +/- 1.84, 3.67 +/- 1.61, and 4.03 +/- 1.81; SUVpeak: 5.60 +/- 2.50, 6.10 +/- 2.80, 5.22 +/- 2.40, and 5.65 +/- 2.68; signal-to-noise ratio: 136.06 +/- 90.58, 136.24 +/- 81.63, 99.52 +/- 53.16, and 107.57 +/- 69.05). Conclusions The MR-gated reconstruction using gated AC reduced the mismatch between MR and PET images and improved the thoracic-abdominal PET image quality in simultaneous PET/MRI systems.