Abstract: We investigated the input–output process with two atoms trapped in an opticalcavity. We demonstrated a photon–logical-qubit hybrid controlled phase flip (CPF) gate in collective-relaxation decoherence-free subspaces (CRDFS) with the input–output process, CRDFS encoding makes our schemes immune to collective relaxation. Based on the CPF gate, efficient scheme of entanglement generation in CRDFS is proposed. Our schemes merely need low-Q and mediate coupling for the physicalsystems, which makes the schemes easier to be identified compared with previous schemes.