In China, urbanization strengthens the water-food-health nexus by driving dietary changes both at home and away from home (AFH). However, few studies have compared the effects of dining location on water footprint generation and/or linked such habits to the prevalence of non-communicable diseases (NCDs), such as hypertension, diabetes, asthma, myocardial infarction, stroke and cancer. Here, household survey data were used to develop a multiple-component urbanization sequence, on which the diet-related water footprint was quantified and the mechanisms under the water-food-health nexus were explored. Significant dietary changes due to urbanization have occurred at home (instead of AHF), and increases or decreases in various food groups are stratified across dining locations. Log mean Divisia index decomposition shows that the diet-structure effect outweighing the intake effect dominates the water footprint changes during China's urbanization. Animal products contribute 92(94)% of the diet-structure effect on net water footprint growth at home(AFH); in contrast, vegetal foods dominate the intake effect, contributing 67(49)%. The at-home water footprint ratio of animal products to vegetal foods is highly related to the prevalence of diabetes, hypertension, cancer, and asthma, and reaching statistical significance. Two urbanization components, namely housing situation and community diversity, serve as the key drivers of water-food-health nexus enhancement in urbanized China. Due to the complexity of water-food-health links, nexus thinking is needed to benefit human health and diet-related water consumption; besides, it may be reasonable to expand current dimension of food-energy-water nexus topic to include health issues.