The invention discloses a fan coil control system for an intelligent building. The fan coil control system comprises multiple fan coils connected in parallel, multiple first switches and multiple intermediate relays, wherein each fan coil is provided with multiple gears; each fan coil comprises an input end and multiple output ends corresponding to the multiple gears; the input end is connected with a live wire, and the output ends of the same gear are mutually connected; the multiple first switches correspond to the multiple gears, and the multiple output ends of each gear are connected with a zero line by virtue of the multiple first switches; the multiple intermediate relays correspond to the multiple gears and are respectively arranged between the live wire and the multiple output end; contact switches of the intermediate relays are connected between the output ends and the intermediate relays; when the first switches are closed, the corresponding intermediate relays are started and opening and closing of the corresponding contact switches are controlled. The fan coil control system can be used for avoiding overburning of the fan coils.