Ensuring performance of applications running on large-scale clusters is one of the primary focuses in HPC research. In this talk, we will show our strategies for performance analysis and optimization of applications in various fields of research using large-scale HPC clusters. Our strategies are designed to comprehensively analyze runtime features of applications, parallelisation strategies of physical models, algorithmic implementations, and other technical details. These three levels of strategy cover platform optimization, technological innovation, and model innovation, and targeted optimization based on these features. State-of-the-art CPU instructions, network communication patterns, and innovative parallel strategies have been optimized for various applications.