A method and apparatus to manage call control in a Computer Telephone Interface (CTI) system includes: a computer terminal to generate a call control message including call control identification information using a CTI application program in response to a call control command from a user, and transmitting the generated call control message; wireless terminals to perform call control upon receipt of the call control message; and an exchange to receive the call control message from the computer terminal, and to maintain the call control message generated by the computer terminal unchanged and to interface it to a corresponding one of the wireless terminals in response to the call control identification information being detected from the received call control message.