Objectives To recognize the nutritional status of hospitalized children by the pediatric nutrition screening-assessment tool, to analyze the differences in clinical outcomes and biochemical indicators under different nutritional status, and to provide evidence for reasonable nutritional intervention. Methods A pediatric nutrition screening-assessment tool, named as Pediatric Nutrition Screening APP, developed by Working group of Pediatrics, Chinese Society of Parental and Enteral Nutrition was used to nutritional screening and assessment of children admitted to the Division of Gastroenterology and Nutrition Xinhua Hospital from March 2018 to October 2020, and to evaluate children at risk of malnutrition and analyze the difference in clinical outcomes and biochemical indicators under different nutritional status. Results A total of 624 children were enrolled, including 368 males and 256 females. There were 158 children in the 0-1 year old group, 95 children in the 1-3 years old group, and 371 children in elder than 3 years old group. Nutrition screening showed that the incidence of malnutrition risk was 56.25%, and the risk of malnutrition was 89.24%, the highest in the 0-1 year old group. Grouped by disease, children with short bowel syndrome have the highest risk of malnutrition at 90.05%, followed by acute pancreatitis at 88.89%, and chronic diarrhea at75.00%. Compared with the non-malnutrition risk group, the children in the malnutrition risk group had significantly longer duration of hospitalization, more hospitalization expenses, higher infection rates, and significantly reduced total protein, albumin, hemoglobin, and 25-(OH)-Vitamin D levels (all P<0.05). Nutrition assessment indicated that the incidence of moderate malnutrition and severe malnutrition were 35.89% and 16.37%, respectively. The incidence of moderate malnutrition and severe malnutrition in the 0-1 year old group were the highest, 34.61% and 36.54%, respectively (both P<0.05). In the normal group, moderate malnutrition group, and severe malnutrition group, the duration of hospitalization, hospitalization expenses, and infection rate stepped up, and the levels of total protein, albumin levels stepped down (all P<0.05). Conclusions The risk of malnutrition and the incidence of moderate and severe malnutrition were higher in children in gastroenterology ward. Children under small age had higher risk of malnutrition and incidence of moderate to severe malnutrition. Under malnutrition status, children had longer hospitalization, increased hospitalization expenses, and higher infection rate, and lower levels of total protein, albumin, and 25-hydroxyvitamin D.