A 10-unit decrease in DQI-I was associated with 24% increase in the likelihood of having NAFLD in the age and sex adjusted model (95% CI: 1.06–1.45, p = 0.009), and the association remained significant when the model was further adjusted for other lifestyle factors, metabolic components and the PNPLA3 genotypes [OR: 1.26 (95% CI: 1.03–1.54), p = 0.027]. This evidence concerns the gene PNPLA3 and metabolic dysfunction-associated steatotic liver disease.