The relationship between changes in body components and the risk of nonalcoholic fatty liver disease (NAFLD) is not fully understood. We investigated the effects of body components and subsequent changes on incident NAFLD at follow-up ultrasound scanning in a longitudinal cohort. We included 9967 participants without NAFLD at baseline who underwent serial health examinations. Sex-specific, weight-adjusted skeletal muscle index (SMI_Wt) was used. Mean follow-up duration was 48.5 ± 33.5 months. NAFLD developed in 2395 participants (24.0%). Body composition was measured using bioelectrical impedance analysis. The following baseline body components were significantly associated with incident NAFLD: the lowest and middle SMI_Wt tertiles in the normal-weight group (adjusted hazard ratio [aHR] = 2.20 and 1.54, respectively), and fat percentage in the normal-weight (aHR = 1.12), overweight (aHR = 1.05), and obese groups (aHR = 1.03) (all P < 0.05). Among 5,033 participants who underwent ≥ 3 health examinations, SMI_Wt increase between the first and second examinations was an independent protective factor against incident NAFLD in non-obese groups (P < 0.05). Increased fat percentage was an independent risk factor for incident NAFLD in all weight categories (P < 0.05). High fat mass at baseline may be a better predictor of incident NAFLD than muscle mass. Reciprocal changes in fat and muscle mass during the first year of follow-up predicted incident NAFLD in non-obese groups.