Background: As obesity becomes more prevalent, non-alcoholic fatty liver disease (NAFLD) is also becoming a major worldwide health problem and the most common cause of chronic liver disease. A new obesity classification method based on a composite index which includes both the body mass index (BMI) and the waist-to-height ratio (WHtR) was recently proposed. However, the usefulness of this approach to assess the risk of NAFLD is unclear. Methods: This is a cross-sectional study of 1,276 adult individuals in Dalian, China. The Mann Whitney U test, χ2 test and t-test were used to compare differences between groups. Binary logistic regression analysis was used to identify independent risk factors. Based on BMI and WHtR tertiles, individuals were divided into five new groups. Spearman correlation and receiver operating characteristic curve (ROC) analyses were performed to compare the NAFLD risk factors among groups based on BMI alone, WHtR alone, or the combination of both indexes. Results: BMI, waistline circumference (WC), WHtR, alanine aminotransferase (ALT), weight, triglycerides (TG), γ-glutamyl transpeptidase (GGT), serum uric acid (SUA), red blood cell (RBC) counts, hemoglobin levels (HGB), fasting blood glucose (FBG) and aspartate aminotransferase (AST) levels were identified as high risk factors for NAFLD (all AUC > 0.7). Logistic regression analysis suggested that BMI and WHtR were independent predictors of the appearance of NAFLD (the ORs for BMI and WHtR were 1.595 and 4.060E-11, respectively; all P < 0.001). The combination of BMI and WHtR tertiles significantly improved the correlation coefficient and Area under the receiver operating characteristic curve (AUC) for NAFLD risk factors in subjects classified as overweight or obese when compared with either BMI or WHtR alone. Conclusions: BMI, WC, WHtR, ALT, weight, TG, GGT, SUA, RBC, HGB, FBG, AST were high risk factors for NAFLD. The composite BMI and WHtR index improved body fat classification and the ability to detect individuals with NAFLD risk, offering a more precise method for the early identification of high- and low-risk NAFLD patients.