Food for special medical purposes (FSMP) has received increasing attention as an enteral nutritional supplement. To investigate the effects of whole nutritional formula (WNF) containing dietary fiber and regular formula on nutritional supplementation and improvement of intestinal microecology, a rat malnutrition model was established with the formulations of WNF, FOS, and SDF (10, 20 g/kg bw) administered by gavage for 30 days. The results showed that the three formulations effectively improved the nutritional status of the malnourished rats, significantly increasing the level of IgG, increasing the abundance of Bacteroidetes, and affecting the content of propionic acid (PRO). The nutritional status of rats is closely related to growth performance, nutritional indexes, and immunoglobulin index, which cause changes in the composition of the intestinal flora. The above results showed that WNF positively affected the nutritional improvement, immune level, and intestinal health of rats. The comprehensive evaluation also suggested that the formulation containing ginseng water‐soluble dietary fiber (ginseng‐SDF) had the most significant effect. WNF foods improve the nutritional and immune factors level of malnourished rats. WNF foods has positive regulatory effect on SCFA and intestinal flora. WNF foods containing ginseng SDF have better improvement effect.