In recent years, the incidence of Crohn’s disease (CD) in the Asia-Pacific region is gradually increasing, and the onset age is decreased at the same time. The relapse of illness and long course of disease easily lead to malnutrition, which will affect the treatment effect of the disease and even worsen the disease. Therefore, it is very important to find the risk factors affecting the nutritional status of children with CD and to carry out effective nursing intervention accordingly. In our study, a total of 180 children with CD who were admitted to our hospital from April 2017 to April 2020 were analyzed retrospectively. The multivariate analysis showed that Pediatric Crohn’s Disease Activity Index (PCDAI), platelet (PLT), hemoglobin (HB), hematocrit (HCT), and albumin (ALB) were independent risk factors affecting the nutritional status of children with CD. The results of AUC showed that combined monitoring of the PCDAI score and the expression of PLT, HB, HCT, and ALB indexes was of great value to evaluate the nutritional status of children with CD. Finally, a series of nursing intervention measures were proposed based on these results. It provides a theoretical basis for improving the nutritional status of children with CD and promoting the clinical outcome.