The present invention relating to computer security field provides a method for safe operation and a system thereof. The method includes: loading the compressed kernel of a safe operating system to a memory of a computer, decompressing the driver of a security device to the memory of the computer; a security master process inquiring the security device and determining whether the security device is legitimate, and if so, the safe operating system creates a security sub-process with which the safe operating system performing information interaction with the security device; verifying whether a user is legitimate, if so, permitting the safe operating system to run properly; otherwise, performing exception handling. The system includes an operating system storage device, a security device and a computer. The presented invention provides a solution that a kernel program of a safe operating system is cooperated with a security device by starting the safe operating system. In the whole process of the computer operation, the kernel of the safe operating system works with the security device, and the security device completes the verification of the user ID and the processing of file data encryption/decryption, which assures the security of the computer operation.