The operation quality of interdisciplinary cooperation platform in higher education is an important factor in determining interdisciplinary development. For this reason, the article establishes the collaboration model of interdisciplinary cooperation platform in higher education with the support of ecosystem theory. In order to realize the efficient use of interdisciplinary scientific research resources, this paper transforms the scheduling of scientific research resources on the interdisciplinary cooperation platform into a multi-objective optimization mathematical model and introduces the simulated annealing algorithm improved by the PSO algorithm to design ISA-PSO algorithm for solving the model. Then the data from China Knowledge Network (CNN) from 2010 to 2024 are selected to analyze the current evolutionary characteristics of interdisciplinary cooperation efficiency in higher education and explore the application effect of ISA-PSO algorithm. The results show that the overall publication volume of the five higher education institutions shows an upward trend, and the average annual growth rate of their total publication volume is 3.07% from 2010 to 2024.The ISA-PSO algorithm obtains the optimal mean value of 15.215 after 32 iterations, which is more efficient than the comparison algorithm. Its application to the scheduling of research resources in interdisciplinary cooperation platform can significantly improve the scheduling efficiency and ensure the effective development of interdisciplinary cooperation mode.