The invention discloses a low-entropy mask disclosure protection method for protecting an SM4 cipher chip, and a system implementing the method. The method comprises the following step: 1) a mask with a length of 16 bytes is selected and divided into four groups, each of which comprises four bytes, and each group of the mask Mi is divided into a quaternion (Mi0, Mi1, Mi2, and Mi3); 2) pre-calculation is carried out on an S box to obtain 16 novel S boxes, the 16 novel S boxes are recorded as Snews, and the 16 Snews are stored; 3) a round function carries out mask updating on data to be protected through the four groups of the masks obtained in Step 1), the masks are selected according to a determined order, and the mask updating is carried out on the data to be protected according to the Snew corresponding to the currently used mask; and 4) after the last round of the mask updating is completed, the mask used for the last round of the mask updating is removed from data obtained through the last round of the mask updating, so that an encrypted ciphertext value is obtained. The method and the system provided by the invention have the advantage that the physical safety of the SM4 cipher chip in an actual application scenario is ensured.