A specific and rational index system is key to scientific research evaluation. According to the characteristics and status of research-oriented hospitals in China, this study aimed to construct a comprehensive and methodical system for scientific research evaluation. Using bibliometric research, we sorted and refined indices for both domestic and international scientific research evaluation systems, established two-dimensional indices of input and output, and constructed the theoretical framework of evaluation after experts. The Delphi method was adopted to determine the evaluation indices at all levels, and the Analytic Hierarchy Process was used to calculate the weights of the indices at all levels. Twenty experts from different medical fields were involved in the 2 rounds study. Altogether, 7 primary, 14 secondary, and 37 tertiary indices were included in the evaluation system. A matrix was built to conduct the maximum eigenvalue, the consistency indices, and the consistency ratio of each expert in the survey. The index weight coefficients of the indices were calculated accordingly. The model exhibited high consistency, and the credibility of the results was verified. The evaluation system for research-oriented hospitals that we established had high specificity, credibility, and rationality. The evaluation system that we established combines some quantitative evaluation indicators, which are subsequently weighted according to their importance in the field of research-oriented hospital. Evaluation index system will provide the practical manner in the future for comparing the potential academic level and impact of research-oriented hospitals. Moreover, further verification, adjustments, and optimization of the system and indicators will be performed in follow-up empirical studies.