Algorithm integration is an important content in developing a comprehensive data processing and analysis system. As the development of a near-space science experiment system, a method to integrate algorithms of multiple types, versions, and functions in a large distributed system is designed to facilitate the algorithm integration in a data processing and analysis system. Parallel development, plug-in calling, flexible expansion, and update iteration of the scientific experiment system are enabled by constructing algorithm plug-ins. The system improved with this method is applied to the ZStack private cloud platform, and the method is verified by calculation and analysis of atmospheric parameters, in-situ detection parameters, and ecological parameters in near-space science experiments.