Abstract Background Lupus mesenteric vasculitis (LMV) as initial presentation is rare, especially in childhood-onset systemic lupus erythematosus (cSLE). It is a critical complication of lupus. At present, the research on cSLE with LMV as the initial presentation is few. The aim of this study was to analyze the clinical characteristics and prognosis of cSLE with LMV in the Chinese population, compared with non-LMV cSLE. Methods A retrospective case-controlled study was conducted on 55 cSLE patients between July 2018 and July 2021. The clinical data, laboratory findings, imaging, treatment, and follow-up data were collected and compared between the two groups of cSLE with LMV and non-LMV. Non-LMV cSLE patients were matched according to the age and sex of LMV patients. Results A total of 11 cSLE patients with LMV as the LMV group and 44 cSLE patients without LMV as the non-LMV group were included. The average age of onset was 12.55 ± 1.57 years old, the male-to-female ratio was 2:9, and high disease activity was observed in the LMV group. Abdominal pain was most common in LMV. Compared with the non-LMV, the percentage of abdominal pain, vomiting, abdominal distension, and diarrhea was higher, and gastrointestinal tract, serous cavity, kidney, and lung damage were higher in the LMV group (P