The risk and influencing factors of prognosis in patients with primary IgA nephropathy (IgAN) were explored. One hundred and twenty-four patients who were diagnosed with IgA nephropathy in West China Hospital of Sichuan University were selected as the study subjects. The baseline data were recorded. All patients were followed up for 3 years. Patients with poor prognosis were defined as poor prognosis group, and the patient with no adverse prognosis was defined as a good prognosis group during the follow-up period. The risk factors that may affect the prognosis of patients with IgAN were analyzed by single factor analysis. The influence of all factors that were statistically significant on the prognosis of the patients was further evaluated by multifactor Cox regression. The single factor analysis and multivariate Cox proportional hazard model showed that patients with 24 h urinary protein, pathological type, Oxford classification (T1+T2), Lee (grade IV) and mesangial IgM deposition were independent factors of patients, and the difference was statistically significant, their P-values were 0.041, 0.046, 0.037, 0.043, and 0.028, respectively. Patients with 24 h urinary protein, pathological type, Oxford classification (T1+T2), Lee (grade IV) and mesangial IgM deposition can be used as independent factors affecting poor prognosis in primary IgAN patients. It provides evidence for early detection of high-risk IgA nephropathy.