The invention presents a network data security system and a protecting method applied in network data transmission. Meanwhile the network data security system includes a client, an authentication dispatching server and a number of distributed servers. The authentication dispatching server includes a first determination device and a user certificate generator; and each distributed server includes a second determination device, a second user certificate generator and a processor. The method for protecting data of the present invention introduces the authentication dispatching server providing the client with a user certificate in a valid period of time and further introduces an updated certificate mechanism for preventing the user certificate from being stolen and further preventing network data from being let out.