Objective To explore the influencing factors of the usage behavior of the scientific research management system and provide references for hospitals in constructing scientific research management systems. Methods Data were collected through questionnaires in April 2024. Based on the unified theory of acceptance and use of technology (UTAUT), the information system success model, and the self-efficacy theory, a research model on the influencing factors of the usage behavior of the scientific research management system among medical staff was constructed from the dual perspectives of users and information systems. The structural equation model was utilized to explore the influencing factors of the usage behavior of the scientific research management system. Results A total of 527 questionnaires were collected. Among them, there were 157 males and 370 females. The overall Cronbach α coefficient of the questionnaire was 0.916, and the KMO value was 0.896. For Bartlett’s test of sphericity (P<0.001). The composite reliability of each latent variable was greater than 0.7, and the average variance extracted was greater than 0.5. Therefore, this questionnaire had good reliability and validity. The research showed that information quality, performance expectancy, effort expectancy, and system quality all had significant positive impacts on the usage intention of users of the scientific research management system (P<0.05). Meanwhile, facilitating conditions and usage intention both had significant positive impacts on the usage behavior of users (P<0.05). Conclusions The construction of the scientific research management system should be guided by management needs, comprehensively sort out the general scientific research work needs of medical staff. Through the apply information-based means, various forms of training, and strengthening policy guidance, the aim is to improve the intelligence level of system operations, enhance the convenience of user self-service, and promote the effective construction of the ecosystem of the scientific research management system.