Based on Cyber-physical Systems (CPS), intelligent manufacturing system is a networked, intelligent and man-machine integrative system consisting of smart machines and human experts, which is a deeply essential amalgamation of production and manufacturing equipments, processes with new-generation Information Communication Technology (ICT). Intelligent manufacturing system is the main orientation of deep integration of informationization and industrialization promoted by Chinese government. Different from traditional information systems, characteristics of intelligent manufacturing system, such as highly integration, information fusion, heterogeneous networks’ interconnection introduce huge security challenges. Based on a serial analysis of concept, technologies, reference architecture and risk factors of Intelligent manufacturing system, a hierarchical security risk matrix and security protection recommendations were proposed.