Background Services for the preclinical development and evaluation of cardiovascular implant devices (CVIDs) is a new industry. However, there is still no indicator system for quality evaluation. Our aim is to construct a service for quality evaluation system for the preclinical research and development of CVIDs based on Fuzzy Analytical Hierarchy Process (FAHP). Methods First, we reviewed the related literature to identify and select possible factors. Second, we developed an analytic hierarchy process framework. Third, we developed a questionnaire based on pairwise comparisons and invited 10 experienced specialists to rate these factors. We then used FAHP to compute the weights of these factors and prioritize them. Finally, to demonstrate the effectiveness of the proposed indicator system, a case study was performed as a practical example. Results Four main indicators (professionalism, functionality, stability and security) and 15 subindicators were selected to form the service evaluation system based on literature review and expert’s proposals. According to the weight calculation data, the order of primary indicators by importance, is professionalism (0.6457), security (0.1193), functionality (0.0958) and stability (0.0596) in sequence. Top five secondary indices are personnel’s technical ability, facility and equipment attractiveness, data auditability, confidentiality capability and professional service procedures. In the case study, FW’s final actual effectiveness value was 0.9076, which is the same as the actual situation. Conclusion The indicator system established in this study is comprehensive, reasonable, reliable and with strong practicality. It is worth popularizing and applying. The implementation of this evaluation system can provide measurable evidence for service demander and a way to improve service quality for suppliers. Electronic supplementary material The online version of this article (10.1186/s12911-019-0773-4) contains supplementary material, which is available to authorized users.