A method and an apparatus for operating a subframe and transmitting channel information for controlling interference in a communication system are provided. If a macro evolved Node B (eNodeB) determines and reports an uplink protection subframe for suppressing uplink transmission to a neighboring eNodeB, transmits scheduling information for uplink data through a downlink subframe corresponding to an uplink protection subframe, and the uplink protection subframe determined by the neighboring eNodeB is reported, a small eNodeB sets the reported uplink protection subframe as a flexible subframe, and uses the flexible subframe for downlink transmission. If the flexible subframe is used for the downlink transmission, a terminal of the small eNodeB measures and transmits non-period channel information in the flexible subframe through at least one uplink subframe.