The invention discloses a system and a method of a mobile phone clock for automatically waking up a user based on a sleep depth period. The method includes that A, a body motion state of the user at current is detected through a body movement detector, and a detection signal is produced and sent to a central processing unit (CPU); B, the detection signal is sent to a sleep period microprocessor by the CPU, judgment for a sleep state of the user at current is carried out by the sleep period microprocessor through the detection signal, and a judgment result is obtained; C, a control command is produced by the sleep period microprocessor according to the judgment result, and a switcher is controlled by a controller to be in a clock mode matched with a sleep mode at current; and D, and the CPU controls a clock wake-up module to remind the user before a preset clock time according to the sleep mode of the user at current and the clock mode. Compared with the prior art, the system and the method greatly guarantee time and the state of deep sleep of the user, are scientized and humanized, can naturally wake up the user in a sleep state, and enable the user to feel relaxed and full of energy and to be in good mood.