Background: The global prevalence of metabolic syndrome (MetS) among young adults has reached 17.4%. We examined associations of three dietary indices and life-course dietary quality trajectories with MetS and its components using a birth cohort. Methods: Participants from rural western China were followed at four time points: infancy, school age, adolescence, and young adulthood (mean age 20 years). Three dietary indices—Dietary Diversity Score (DDS), healthy Plant-based Diet Index (h-PDI), and EAT-Lancet score—were compared. Group-based trajectory modeling (GBTM) characterized dietary quality trajectories across the four stages. Results: Among 741 young adults (53% male), 29 (5.1%) had MetS, 217 (38.2%) had at least one metabolic abnormality, and 122 (21.1%) were overweight or obese. Higher DDS was inversely associated with overweight/obesity (T3 vs. T1: OR 0.26, 95% CI 0.10–0.69) and high waist-to-height ratio (WHtR) (OR 0.26, 95% CI 0.09–0.73). Higher h-PDI was positively associated with high WHtR (OR 3.01, 95% CI 1.11–8.15). The EAT-Lancet score was inversely associated with overweight/obesity (OR 0.34, 95% CI 0.15–0.78). After stratified Benjamini-Hochberg correction, these four associations remained significant (adjusted P [ Q ] values 0.016–0.046). Among 298 participants with complete dietary data, two trajectories were identified: increasing (53.0%) and declining (47.0%). The increasing trajectory was associated with lower odds of overweight/obesity (OR 0.34, 95% CI 0.15–0.77). Conclusion: In this rural Chinese cohort, higher DDS and EAT-Lancet were associated with lower odds of overweight/obesity after FDR correction. An increasing dietary trajectory from infancy to young adulthood was also protective. All three indices showed similar discriminative ability. These findings support life-course dietary health promotion.