To analyze the scientific research performance of science, engineering and medicine interdisciplinary projects in a hospital from 2018 to 2020, and to provide reference for optimizing the management of these projects，the evaluation index system was constructed based on the input-output data, and the data envelopment analysis (DEA) BCC model was used to measure its comprehensive efficiency, pure technical efficiency and scale efficiency. From 2018 to 2020, the average comprehensive efficiency of New Medicine Joint Fund exceedes 0.5, and the effective proportion of DEA fluctuates around 25%. In 2018, 2019 and 2020, the effective proportion of DEA for cultivation projects is 15.6%, 22.97%, and 31.91% respectively. The effective proportion of DEA for innovation team projects is 100% in 2018, and 0 in 2019 and 2020. The effective proportion of DEA for important direction projects is 66.67%, 28.57%, and 37.5% respectively. 1 (25%) innovation team project and 5 (23.81%) important direction projects have redundant research funding. 3 (75%) innovation team projects, 12 (57.14%) important direction projects and 125 (75.3% ) cultivation project have insufficient output. The overall scientific research efficiency of the Fund is on the rise, and the whole process management can be optimized by dynamically adjusting the project settings, focusing on the cultivation of young talents, perfecting the multidisciplinary cross-project platforms and mechanisms, optimizing the appraisal and evaluation system, and focusing on the transformation and application of the achievements, and other initiatives.