Child undernutrition is a major health problem in Malawi. We assessed the association between maternal autonomy and child stunting in Malawi. We utilized nationally representative pooled cross-sectional data from the 2010 and 2015/16 Malawi Demographic and Health Surveys (MDHS), which included 7348 mother (28.1 ± 6.8 years, range 15-49 years)-child (27.6 ± 16.7 months, range 0-59 months) pairs. Maternal autonomy composite scores captured decision-making power, tolerance of domestic violence, and financial independence. The nutritional outcome measure was stunting (height-for-age z score < - 2). Logistic regression assessed associations between maternal autonomy and stunting, and dominance analysis evaluated the relative importance of the associated factors. From the two surveys combined, 39.2% were stunted. Stunting decreased from 45.0% in 2010 to 34.6% in 2015/16; concurrently, maternal autonomy improved and was evidently associated with stunting (aOR = 0.81, 95% CI = 0.71, 0.93; p = 0.002). However, this association was probably mediated by other factors associated with improved child nutrition, including maternal education and family wealth, which, along with child age, were associated with stunting in the dominance analysis. Concurrent interventional programs may also have contributed to the decrease in stunting between the surveys, thus moderating the effect of maternal autonomy.