Doctor-patient relationship is complicated system engineering, involving many influence factors. Recent doctor-patient relationship researches mainly focus on two players which are doctors and patients. It's a comparatively narrow sense. Based on researches before, this paper proposes five main influence players of doctor-patient relationship:government, hospital administrator, medical staff, media, and patient. According to these five players, and consulting with other experts, we systemize the index system proposed by other researchers, and then initially establish a new doctor-patient relationship index system by using factor analysis. Furthermore, we study the structure and reasonableness of the index system with interpretative structural modeling (ISM). The proposed comprehensive doctor-patient relationship index system is worthy in assessment and influence factor analysis of doctor-patient relationship. And it contributes to the establishment of cross-region general doctor-patient relationship index system.