In this paper, coordinate interleaved orthogonal frequency division multiplexing with index modulation‐ (CI‐OFDM‐IM) based orthogonal cooperative system (OCS) is proposed, where the source activates half of the subcarriers to convey the symbols in the first time slot (TS). The subcarrier activation patterns (SAPs) are also exploited to convey additional information. In the second TS, the relay amplifies and forwards the received signal to the destination, meanwhile, the source activates the remaining half of the subcarriers to convey the new symbols to the destination. Since the source and relay transmit different symbols to the destination on the different subcarriers in the second TS, the mutual interference is avoided at the destination. Compared with the current OFDM based OCS, the proposed CI‐OFDM‐IM‐based OCS can achieve a higher spectral efficiency, since the SAPs are exploited to convey additional information. Furthermore, the CI‐OFDM‐IM‐based OCS can achieve additional power gain for a certain average transmit power, since the power of inactive subcarriers can be reallocated on the active subcarriers. The optimal constellation rotation, in the sense of maximizing the minimum Euclidean distance between the symbols conveyed on a subcarrier over two TSs, is provided to optimize the performance of CI‐OFDM‐IM‐based OCS. Simulation results show that the proposed CI‐OFDM‐IM‐based OCS achieves a better trade‐off between spectral efficiency and bit error ratio performance.