The trend towards diversified dietary consumption in China has resulted in a rising prevalence of nutrition and health problems, which places a significant burden due to medical expenditures. This burden presents an economic obstacle for the nation and households to progress toward prosperity. In this study, we employ a footprint-based approach to estimate the changes in medical investment attributed to dietary structural modifications in China from 1992 to 2021. We predict China’s dietary structure and consequent medical expenditures over the next decade. Our findings reveal that the dietary diversity index in China has increased by 0.397 over the past 30 years and that urban-rural and geographical nutritional disparities are narrowing. The ratio of national financial medical expenditure to total expenditures generated by the change in diet structure has increased by 18.06%, and the per capita healthcare expenditure of the population as a share of total consumption expenditures has increased by 29.46%. The change in the dietary structure of the population contributed to 28.77% of the increase in national financial medical expenditure in China between 1992 and 2021, and 33.40% of the increase in per capita health care expenditure of the population and in 2030. These two values will change to 27.61% and 39.68%, and the national financial medical expenditure generated by the change in dietary structure from 2022 to 2030 will also increase. National financial medical expenditure will increase by 152.8 billion yuan, and per capita healthcare expenditure of the population will increase by 310 yuan. The main source of this contribution is the rising scale of animal foods and sugar consumption. The positive effect of animal foods and sugar on the growth of medical expenditures will continue to expand, but the negative effect of plant-based foods, such as cereals and fruits and vegetables will largely offset this positive effect. Promoting a geographic balance of dietary and medical resources, stabilizing national cereals production, and reducing consumption of animal foods and sugars by several units could help offset the medical inputs from changes in the dietary structure. These findings illuminate the socio-economic impact of dietary changes.