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We propose a scheme for realization of three-qubit controlled-phase gate via passing two three-level atoms through a high-Q optical cavity in a cavity QED system. In the presented protocol, the two stable ground states of the atoms act as the two controlling qubits and the zero- and one-photon Fock states of the cavity-field form the target qubit, and no auxiliary state or any measurement is required. The numerical simulation shows that the gate fidelities remain at a high level under the influence of the atomic spontaneous emission, the decay of the cavity mode and deviation of the coupling strength. The experimental feasibility of our proposal is also discussed.