Objective: To explore the prognosis factors that influence the postoperative survival rate in patients with malignant solitary pulmonary nodules and to provide a reference for the prognosis risk stratification of early lung cancer patients. Methods: In this study, we retrospectively reviewed 172 patients who were admitted to Peking University First Hospital from April 2006 to December 2013. All cases were radiologically defined as solitary pulmonary nodule and were pathologically confirmed to be stage Ⅰa non-small cell lung cancer after surgical procedure. The patients’ clinical and follow-up data were summarized and analyzed. The relevance between survival time and factors that may affect patients’ prognosis was evaluated, which included gender, age, clinical symptoms, smoking history, comorbidity index, tumor biomarkers, nodule type, type of surgery, nodule location, nodule histopathological type, nodule size, histopathological differentiation grade, proliferating cell nuclear antigen Ki-67 expression level and epidermal growth factor receptor (EGFR) gene mutation. Kaplan-Meier survival analysis, Cox univariant and multivariant regression analysis were conducted to evaluate the factors affecting prognosis. Results: The 3-year overall survival rate of the atients with malignant solitary pulmonary nodules was 93.6%, and the 5-year overall survival rate was 89.8%. Kaplan-Meier survival analysis and Cox univariant regression analysis showed that the overall survival rate of the male patients was significantly lower than that of the female patients. In addition, the elderly patients with histopathology characterized as high Ki-67 proliferation index were also associated with the worse overall survival (P<0.05). Cox multivariant regression analysis demonstrated that age more than 65 years as well as the high Ki-67 expression level were independent risk factors for overall survival in patients with malignant solitary pulmonary nodules (age: P=0.023, HR=3.531, 95%CI 1.190-10.472; Ki-67: P=0.004, HR=1.021, 95%CI 1.007-1.035). Conclusion: For patients with malignant solitary pulmonary nodules, with pathological defined as stage Ⅰa non-small cell lung cancer, age, gender and Ki-67 expression levels might be important prognostic factors. Comprehensive consideration of Ki-67 proliferation index and clinical pathological features may help to stratify the prognosis more accurately and guide the selection of appropriate therapeutic strategies, which needs to be verified by multi-center studies.