Henoch-Schönlein Purpura (HSP) is a systemic small vessel, leucocytoclastic vasculitis disease affecting children, and the abdominal pain and joint pain are its classic triad. Here, we studied the correlation between serum cystatin C (CysC), thrombomodulin (TM), and T lymphocyte subsets in HSP cases, and the diagnostic values of these indices. A total of 120 HSP children treated at The 940th Hospital of Joint Logistics Support Force of the Chinese People's Liberation Army from January 2019 to May 2020 participated in this study. Another 64 healthy children receiving routine physical examination in the same time range were enrolled as a control group. In the early morning of the next day after admission, the cubital venous blood was collected. The serum levels of CysC were measured by immunoturbidimetry, the TM was detected using ELISA, while the T lymphocyte subsets were detected by flow cytometry. Univariate and multivariate logistic regression analyses were performed to determine the susceptibility factors. The receiver operating characteristic (ROC) curves were plotted to evaluate the predictive values of CysC, TM and T lymphocyte subset alone and their combination for HSP. The serum levels of CysC, TM, and cluster of differentiation 8 (CD8 + ) of HSP children significantly increased and their CD3 + , CD4 + levels and CD4 + /CD8 + ratio significantly decreased compared with those of control group ( P <0.05). The serum levels of CysC and TM were significantly correlated negatively with CD3 + , CD4 + levels and CD4 + /CD8 + , whereas positively with CD8 + level ( P <0.05). Diet, infection, drugs, exercise-induced tiredness, air pollution, family environment, family inheritance, age, winter and spring were the susceptibility factors for children with HSP. The diagnosis using CysC, TM and T lymphocyte subsets had an AUC of 0.901, sensitivity of 93.1%, and specificity of 90.2%. In conclusion, the combined monitoring of serum CysC, TM, and T lymphocyte subsets in children with HSP can raise the accurate diagnosis rate.