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Background The clinical features of upper gastrointestinal (L4) Crohn's disease (CD) and its subtypes, along with the associated and nutritional status, remain poorly described. Our aim was to evaluate the clinical characteristics of L4 CD phenotype and its subtypes at diagnosis, and their relationship with the nutritional status. Methods A retrospective study was conducted on 869 CD patients diagnosed between 2013 and 2019, and the association between the clinical characteristics and nutritional status of L4 patients was determined using Random forest importance ranking and logistic regression. Results The majority of the patients (59.72%) presented L4 lesions, of which 335, 158 and 26 had proximal ileal, jejunal and esophago-gastroduodenal (EGD) lesions respectively. L4 patients were predominantly male (OR 2.07), smoker (OR 1.80), and had higher body weight and BMI, longer disease course, and stricturing disease (OR 1.88). Furthermore, the serum albumin level, body weight and disease course showed higher MDG in the random forest importance ranking test for L4 CD and L4-proximal ileal types. According to logistic regression, body weight (OR 1.054), disease course (OR 1.010), stricturing behavior (OR 4.998) and tomato intolerance (OR 1.313) were the independent risk factors for L4. In addition, body weight (OR 1.042) and stricturing behavior (OR 3.152) were the relevant factors for proximal ileal subtype, and stricturing behavior (OR 4.206) and perianal disease (OR 0.339) for jejunal subtype. Conclusions L4 disease has a higher incidence rate compared to the non-L4 CD, and mainly affects males, and those with prolonged disease course, stricturing behavior, higher weight, BMI, albumin levels and food intolerance (FI).