Objective To explore the application value of index evaluation method in the quality evaluation of infectious disease reporting management. Methods A total of 55 hospitals at different levels were selected and investigated by contents of organizational system construction, registration and feedback of notifiable communicable disease, reporting rate, reporting timeliness rate, completeness and accuracy of reporting cards. Comprehensive evaluation index system to the management and quality of notifiable communicable diseases reporting in medical institutions was established. Expert interview method was performed to determine the index system and weight, comprehensive evaluation index was conducted to evaluate management and quality of notifiable communicable disease reporting. Results The comprehensive evaluation index of 55 institutions was 0.9141, there was significant difference in different areas (F=2.858, P=0.004), but wasn’t at different levels (F=0.126, P=0.944). The comprehensive evaluation index among institutions with higher reporting rate or reporting timeliness rate were not significantly higher than institutions with lower. Conclusion The comprehensive evaluation index system is practical and operable to assess management and quality of notifiable communicable disease reporting in medical institutions.