Background: This study analyzes the prognostic factors affecting the survival rate of root-resected molars by using a representative population-based dataset. Materials and Methods: A total of635,216 eligible patients were enrolled from a representative cohort composed of one million of Taiwan’s population. The tooth-related factors influencing the survival rates of root-resected teeth were examined on 516 molars, in 492 patients. Cox regression was performed to statistically analyze the factors. Results: The overall survival rate for the root-resected molars was 91.7%. Of the analyzed factors with respect to root-resection procedures, whether or not concomitant flap surgery was performed in the medical institutions, the dental arch and tooth location demonstrated a considerable influence on the treatment and decision-making. The main reasons and results of root-resected molars receiving root-resection therapy in hospitals were the periodontal-compromised conditions, whereas, the root-resected molars that received root-resection therapy in private practice clinics were caused by caries/endodontic reasons. After adjusting for other factors, in the outcome of root-resected molars, a higher risk of extraction occurrence was seen in hospitals than in private practice clinics (hazard ratio = 2.03; 95% Cl = 1.04 to 3.98; P = 0.039). Conclusions: Of the analyzed prognostic factors, medical institutions significantly affect the treatment decision and survival of root-resected molars. Therefore, a comprehensive evaluation, risk assessment, and treatment plan should be executed before the root-resection procedure is performed.