Women's autonomy in healthcare decision-making is crucial not only for improving maternal health but also enhancing their overall health and well-being. However, most studies focused solely on fertility, child health, or maternal healthcare use, often overlooking the broader aspects of women's health. Due to this reason, the magnitudes and factors associated with women's autonomy in other types of healthcare remain unclear. Therefore, this study aimed to estimate the magnitude and identify factors associated with healthcare decision-making autonomy among married women in Indonesia. A national cross-sectional study was conducted among married women using the Indonesia Demographic and Health Surveys 2017. Women's healthcare decision-making autonomy was measured based on responses regarding the individual typically responsible for making healthcare decisions on behalf of the respondent. Potential factors, such as intrapersonal, interpersonal, community, and policy-related were obtained. Multinomial logistic regression was used to determine the associations between potential factors and outcomes. The odds ratio (OR) and 95% confidence intervals (CI) of the analysis were reported. The respondents in this study comprised 16,050 married women across 34 provinces in Indonesia. Most respondents (46.4%) reported making healthcare decisions independently. The result showed that several factors were associated with either women's full autonomy or jointly with the husbands in the healthcare decision-making. These factors included ownership of mobile telephones, urban living, residency in Java, Bali, Sulawesi, Maluku and Papua islands, participation of women in decision-making on how to spend their earnings, on large household purchases, no financial barrier in accessing treatment, and independence in visiting a medical center. Public health interventions should focus on vulnerable women, such as those who live in rural areas, participate less in the decision-making of earnings spending and household purchase, and are incapable of visiting a medical center alone to increase the healthcare decision-making autonomy. Collaborative efforts with health facilities in each region can support the implementation of this intervention.