The infrared detector is used for sea target search, which can assist humans in searching suspicious objects at night and under poor visibility conditions, and improving search efficiency. This paper applies for interrupt and stack technology to solve problems of data losses that may be caused by one-to-many multi-byte protocol communication. Meanwhile, this paper implements hardware and software design of the system based on industrial-grade ARM control chip and uC / OS-II embedded operating system. The control system in the sea target search system is an information exchange and control center of the whole system, which solves the problem of controlling over the shooting angle of the infrared detector in the process of target search. After testing, the control system operates stably and reliably, and realizes rotation and control functions of the pan/tilt platform during automatic search, manual search and track.