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In this paper, we consider dynamical Chern-Simons gravity with the identification of the scalar field coupled though the Pontryagin density with the axion dark matter, and we discuss the effects of the parametric resonance on gravitational waves (GWs). When we consider GWs in a coherently oscillating axion cloud, we confirm that significant resonant amplification of GWs occurs in a narrow frequency band, and the amplification is restricted to the late epoch after the passage of the incident waves. We also identify the condition that an axion cloud spontaneously emits GWs. Once we take into account the randomness of the spatial phase distribution of the axion oscillations, we find that the amplification is suppressed compared with the coherent case, but significant amplification of GWs can still occur. We also examine whether or not the amplification of GWs is possible in the present universe, taking into account the history of the universe. We find that resonant amplification is difficult to be tested from GW observations in the standard scenario of the axion DM model, in which the axion is the dominant component of DM. However, there is some parameter window in which the resonant amplification of GWs might be observed, if the axion is subdominant component of DM, and the axion cloud formation is delayed until the Hubble rate becomes much smaller than the axion mass.