The paper presented the theoretic basis for the comprehensive hospital evaluation system, and initiated the indicator system for hospital comprehensive evaluation results with both Delphi method and the balance scorecard. Two rounds of experts consultation have decided to evaluate hospital comprehensive strengths from such aspects as hospital resources deployment, business process, financial standing, customers, customers, public welfare and development potential of the hospital. Under these grade-1 indicators are 13 grade-2 ones and 83 grade-3 ones. The importance, operability and sensitivity of these indicators are accepted by experts unanimously.