Focusing on the multi-scale structures of complex systems, the study has identified the dominant mechanisms in gas-solid flow, gas-liquid flow, emulsion, nano-/micro-flow and biological interfacial process, and established the stability conditions in these systems by analyzing the compromise between the respective mechanisms. Based on these findings, a multi-scale analysis and simulation methodology of general significance is proposed and the corresponding computational methods and high performance computing systems developed. The study has earned international attention and recognition. The research group was invited to compile two special issues on this topic in Chemical Engineering Science, the leading journal of the field, and the research achievements have been applied successfully in several key R&D projects of giant enterprises worldwide.