An intelligent message processing system includes: a service provider server configured to generate and send a message related to a customer service; a user terminal configured to receive a beginning message from the service provider server, make the beginning message pop up based on user situation information, and perform automatic dialogue through an interactive application program interface (API) when a message is received from an intelligent proxy server after the user selects the beginning message; and an intelligent proxy server configured to act as a proxy for processing the message related to the customer service instead of the service provider server through the interactive API by communicating with the user terminal, receive an additional/following-up service message about the user from the service provider server, and perform automatic dialogue with the user terminal through the interactive API based on the additional/following-up service message when the user selects the beginning message.