In order to provide guidance for effectively improving the performance of clinical research expenditures, this paper investigates the potential issues existing in the fund usage through a case study of the fund management situation from 2009 to 2019 in the clinical departments of a grade-A specialized tertiary hospital in Nanjing. During July and August 2019, a self-designed questionnaire survey was conducted among researchers across the whole institution for the purpose of basic information collection; In the meantime, Colaizzi’s phenomenological methodology was employed to qualitatively analyze the information acquired by the semi-structured in-depth interviews with 33 fund users in the institution. People with intermediate-to-senior qualifications, bachelor’s degrees or above, and vice-senior titles serve as the main force of research management funds. The distribution of actual received amount of research funds and high-quality publications showed differences with statistical significance among various departments (P<0.05). There is a common surplus of research funds across all the departments, and no significant interdepartmental differences in the proportion of surplus over the total funds were identified. The establishment of project funds should be inclined to young professional. The main causes of the underuse of the research funds include fund cross-utilization, overfunding that exceeds actual demands, lack of convenient implementation routes and active research atmosphere. It has been shown by the in-depth interviews that personal interest, self-actualization, and demand for promotion of profession title act as the positive factors for robust utilizations of research funds, while busy engagements and lack of objective conditions are the main negative factors.