Suitable nutritional diets have been widely recognized as important measures to prevent and control non-communicable diseases (NCDs). However, there is little research on nutritional ingredients in food now, which are beneficial to the rehabilitation of NCDs. In this paper, we profoundly analyzed the relationship between nutritional ingredients and diseases by using data mining methods. First, more than 7000 diseases were obtained, and we collected the recommended food and taboo food for each disease. Then, referring to the China Food Nutrition , we used noise intensity and information entropy to find out which nutritional ingredients can exert positive effects on diseases. Finally, we proposed an improved algorithm named CVNDA_Red based on rough sets to select the corresponding core ingredients from the positive nutritional ingredients. To the best of our knowledge, this is the first study to discuss the relationship between nutritional ingredients in food and diseases through data mining based on rough set theory in China. The experiments on real-life data show that our method based on data mining improves the performance compared with the traditional statistical approach, with the precision of 1.682. In addition, for some common diseases, such as diabetes, hypertension and heart disease, our work is able to identify correctly the first two or three nutritional ingredients in food that can benefit the rehabilitation of those diseases. These experimental results demonstrate the effectiveness of applying data mining in selecting of nutritional ingredients in food for disease analysis.