Abstract A protocol is proposed for generating three‐particle Knill‐Laflamme‐Milburn (KLM) states in a system composed of two frequency‐tunable flux qubits and a coplanar waveguide resonator. With the help of the counter‐rotating interaction, the protocol for generating three‐particle KLM states can be realized. The numerical results reveal that the protocol is robust against the effects induced by decoherence and frequency‐tuning operations. It is hope that the protocol provides an alternative method to generate entangled states.