Using the atomic state encoded in the collective-rotating decoherence-free subspace (CRDFS), two methods to construct the hybrid-controlled-phase-flip gate between photon and the single logic qubit are presented assisted by the cavity inputoutput process. Then, ways to realize the common single-qubit operations in CRDFS are given out. Based on the former gate and single-qubit operations, methods to construct the parity gate and controlled-phase gate in CRDFS are discussed. Next, two ways to realize the Bell-state measurement and the approach to realize quantum information transfer in CRDFS are proposed. Final discussion and numerical simulation reveal that our work is feasible and useful for quantum information processing tasks in CRDFS.