The invention discloses an embedded system and an implementation method of a secure operating system. A hardware system comprises an encryption chip which supports an RSA asymmetric encryption algorithm and can provide 2048-bit private keys, and a protected nonvolatile memory. A software system carries out asymmetric encryption algorithm authentication on progresses on the basis of a Linux operating system, operations related to the private keys are accomplished in a specific memory region, namely a section with a hidden address, of the protected nonvolatile memory, only the progresses which pass authentication can run in the secure operating system at the moment, and the progresses which do not pass authentication can be killed. Due to the fact that the secure operating system has the memory protection function, the key authentication function and the like, the secure operating system is a trusted computing framework system, and has high safety. The secure operating system is mainly used in the special fields, such as the security field and confidentiality field, and can be matched with hardware systems of universal PCs, embedded tablet personal computers and the like.