The coherent potential approximation (CPA) within full counting statistics (FCS) formalism is shown to be a suitable method to investigate average electric conductance, shot noise as well as higher order cumulants in disordered systems. We develop a similar FCS-CPA formalism for phonon transport through disordered systems. As a byproduct, we derive relations among coefficients of different phonon current cumulants. We apply the FCS-CPA method to investigate phonon transport properties of graphene systems in the presence of disorders. For binary disorders as well as Anderson disorders, we calculate up to the $8$-th phonon transmission moments and demonstrate that the numerical results of the FCS-CPA method agree very well with that of the brute force method. The benchmark shows that the FCS-CPA method achieves $20$ times more speedup ratio. Collective features of phonon current cumulants are also revealed.
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