While human beings enter in high spirits the era of network-based digital economy and enjoy to their hearts’ content the wonderful material and cultural life delivered by science and technology, they encounter the problem of cyberspace security, which haunts, like a ghost, in both the physical and virtual worlds of the Internet of Everything, constituting the “Achilles’ heel” of the network information society and the digital economy. This is due to of the four theoretical and engineering security problems arising from the related original sources which are difficult to break through: 1. Loopholes: Loopholes result from the hardware and software defects that are unavoidable in the current stage of science development, though hardware and software are the bedrock of the information era. 2. Backdoors and Trojans: They are usually planted on the hardware during the making or supply process and are impossible to be eradicated due to the totally open ecosystem—the global value chain characterized by division of labor across countries, industries, and even within a product. 3. Lack of theoretical and technical means to thoroughly examine the complicated information system or control the hardware/software code configuration of devices in the foreseeable future. 4. Backdoors and loopholes polluting the cyberspace from the source. This is due to the above-mentioned causes, which lead to ineffective quality assurance and supervision during the design, production, maintenance, application, and management processes.