Women's nutritional health is significantly influenced by their social standing, especially in low- and middle-income countries where patriarchal structures restrict women's decision-making. In India, women have limited autonomy over personal and domestic matters, which restricts their decision-making power and access to resources. In this context, this study investigates the relationship between women's empowerment and their nutritional health in India. We used nationally representative data from the most recent iteration of the National Family Health Survey (NFHS-5), 2019-2021. Women's autonomy was measured using a composite Women's Autonomy Index (WAI), encompassing decision-making power, asset ownership, and freedom of movement. Logistic regression models were used to estimate the association between WAI and underweight (BMI < 18.5 kg/m), controlling for sociodemographic and household factors. Robustness checks were performed, which included modelling continuous BMI, using alternative autonomy specifications (WAI Modified), and performing stratified analysis by urban-rural residence. A total of 14.0% (95% CI 13.6, 14.4%) of the study participants were underweight. Higher autonomy was associated with significantly lower odds of being underweight (adjusted OR: 0.951; 95% CI 0.923, 0.980). The margins analysis indicated that the predicted underweight prevalence was 9.5% among women with the highest autonomy scores compared to 16.3% among those with no/low autonomy. Continuous BMI models showed a positive gradient, with BMI increasing by approximately 1.5 kg/m across the full range of autonomy scores. Stratified analysis revealed stronger autonomy effects in urban areas. These associations remained robust when we used an expanded autonomy measure that incorporated joint decision-making. Women's age, educational status, work status, husband's educational level, place of residence, household size, and household wealth were strong predictors of women's nutritional status. We find a strong association between women's autonomy and nutritional status, with higher autonomy reducing the risk of undernutrition. In addition, regional and socioeconomic disparities are also factors that affect women's nutritional status. Policy interventions that ameliorate women's decision-making power, asset control, and mobility can effectively address undernutrition among women and promote broader health gains.