Objective To explore the influencing factors for financial risk caused by Medical Treatment Partnerships business in the leading hospital of Medical Treatment Partnerships. Methods A mixed method of questionnaires and expert interviews was adopted to conduct investigation on 206 leading hospitals of Medical Treatment Partnerships in X province, concerning types and scales of Medical Treatment Partnerships, leading hospital grade, the occurrence of financial risk events due to Medical Treatment Partnerships business, and financial loss events, etc. The financial risk scores were compared between leading hospitals of Medical Treatment Partnerships with different types and scales of Medical Treatment Partnerships and hospital grade, and a rank⁃based regression model was established to quantify the correlation effect. Results There was no statistically significant difference in financial risk between leading hospitals of Medical Treatment Partnerships with different scales of Medical Treatment Partnerships and hospital grade (P>0.05). There was a statistically significant difference in financial risk between leading hospitals of Medical Treatment Partnerships with different types of Medical Treatment Partnerships, and financial risks of leading hospitals of Medical Treatment Partnerships of loose, tight, and high⁃tight Medical Treatment Partnership increased in turn (P<0.05); furthermore, financial risk levels of leading hospitals of tight and high⁃tight Medical Treatment Partnerships were 89.15% and 133.67% higher than those of loose Medical Treatment Partnerships, respectively. Conclusion The degree of Medical Treatment Partnerships integration is closely related to financial risk of leading hospital. Relevant government departments should improve the external supervision system of Medical Treatment Partnerships, improve the supporting system of financial management, strictly approve the establishment of high⁃tight Medical Treatment Partnerships, and establish a stable and long⁃term investment mechanism. Leading hospital of Medical Treatment Partnerships should strengthen internal control and financial risk management.