A simple scheme for the generation of three-qutrit singlet state is proposed, which is based on the cavity quantum electrodynamics (QED) by means of the two-photon transitions. Here a Ξ-type three-level atom originally prepared in the excited state sequentially resonates with three cavities prepared in suitable initial states (vacuum state or one-photon state). The singlet state with maximum fidelity can be obtained by selecting the interaction time between atom and cavity field and probing the atomic states. In addition, the influence of atom-cavity coupling constant on fidelity and the practical feasibility of the proposed scheme are discussed. The results show that in the case of detuning equal to zero, the fidelity is more sensitive to the atom-cavity interaction time for a larger coupling constant.