The SECS Ⅰ and Ⅱ Protocol has been widely used for the TFT LCD and semiconductor industry. This paper shows how the SECS protocol is implemented for data communications between the Host (CAM) and the TFT LCD equipments. In addition, this study introduces a way to apply the SECS protocol to the manufacturing systems control. It provides better throughput in terms of production and faster control of the automated TFT LCD manufacturing system by way of shortcut and distribution of control and data communications. The SECS protocol is successfully used for the control of the real TFT LCD manufacturing system.