Background: Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most common chronic liver disease in China. Our study aimed to evaluate the screening value of the fatty liver index (FLI), hepatic steatosis index (HSI), lipid accumulation product (LAP), visceral adiposity index (VAI), and Zhejiang University index (ZJU), as well as other single indicators for MAFLD. We aimed to find the optimal screening tool and its appropriate cut-off values for rural Uyghur adults. Methods: We completed a survey of 14,321 Uyghur adults in 51 groups in Kashgar, Xinjiang, in 2016 using a typical sampling method, with 12,794 patients ultimately included in statistical analyses. Fatty liver was diagnosed using ultrasonography. Results: The prevalence of fatty liver disease (FLD) and MAFLD was 16.73% and 16.55%, respectively, and the FLI, HSI, LAP, VAI, and ZJU were all independently associated with an increased risk of MAFLD. The areas under the receiver operating characteristic curves (AUCs) of the FLI for diagnosing MAFLD in men and women were 0.853 and 0.847, respectively. The AUCs of the body mass index (BMI) for diagnosing MAFLD in men and women were 0.850 and 0.852, respectively. Compared with other metabolic-related markers, FLI had the largest AUC. In men, the optimal cut-off values of FLI and BMI for diagnosing MAFLD were 45 (sensitivity 84.83%, specificity 69.57%) and 27.4 (sensitivity 78.47%, specificity 76.30%), respectively. In women, the optimal cut-off values of FLI and BMI for diagnosing MAFLD were 45 (sensitivity 80.11%, specificity 74.23%) and 28.0 (sensitivity 79.56%, specificity 75.41%), respectively. In men and women, an FLI score of < 30 ruled out MAFLD, while a score of ≥ 50 was a basis for diagnosis. Conclusion: FLI and BMI had good screening ability for MAFLD and were superior to HSI, LAP, VAI, and ZJU in both sexes.