The invention, related to information security field, discloses a method for protecting software, and device and system thereof. The method includes that a security device is connected with a terminal device; the security device receives service instruction, determines whether the clock inside the security device is activated, reads the current time of the clock and determines whether the current time is valid; if so, the security device executes the service instruction and returns the executing result to the terminal device; otherwise, the security device returns false result to the terminal device. The invention provides more secure service to the protected software, meanwhile, extends lifetime of the security device.