The invention relates to a VPN processing module of short messages and a processing method thereof. The processing method comprises that: step 1, the VPN processing module judges whether a number of a receiving subscriber in a short message is a mobile phone number after receiving the short message, if so, a step 3 is executed, and if not, a step 2 is executed; step 2, whether the corresponding mobile phone number of the number of the receiving subscriber exists in the VPN processing module is inquired, if so, a number of a sending subscriber is replaced by the corresponding number VPN short code of the number of the sending subscriber, and the step 3 is executed, and if not, the step 3 is directly executed; step 3, the VPN processing module sends the short message to a short message center for distributing the short message. The method of the invention does not need to modify the networking of the system or other relevant element locations in the network, does not lose the information content carried by the original short message, does not influence the use habits of users, and is easy to realize, thus leading a calling user to normally send the short messages through a VPN short code or a phone number of the called user.