We propose a scheme for implementing a three-qubit controlled-Not-Not (CNNOT) gate and a two-qubit SWAP gate between atoms and single-photon pulse through cavity QED. In the scheme, we can one-step realize multiple-qubit GHZ state and two-qubit Bell state by applying multiple-qubits CNNOT gate. We have also shown that our scheme would be robust against practical imperfections in current cavity QED experiment setup through simple numerical estimates. Finally, we provide the current parameters to show that our scheme is feasible.