The Chinese food system has expanded its focus from aiming to solve food problems to tackling current health and environmental issues. The Chinese diet has increased in quantity and improved in safety, but there is still room for improvement in terms of health and sustainability. This study used Chinese dietary data provided by the Global Diet Database to analyze the changes in China’s dietary structure from 1990 to 2018 and highlight differences in urban and rural areas and across education levels. Findings show that the intake of food and beverage, macronutrients, and micronutrients in urban areas is higher than in rural areas. The difference in food and beverage intake between urban and rural areas is significant. The dietary gap between urban and rural areas has gradually widened. The difference in food and beverage and macronutrient intake across education levels is significant, but the difference in micronutrient intake is not significant. The gap in dietary structure across educational levels is relatively stable. These results indicate that the dietary structures of different groups in China are uncoordinated. We propose policies covering agricultural production, supply chain infrastructure, public institutions, education, and public awareness to build a sustainable food system with a healthy dietary pattern.