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The clock transitions (CTs) of central spins have long coherence times because their frequency fluctuations vanish in the linear order of external field noise (such as Overhauser fields from nuclear spin baths). Therefore, CTs are useful for quantum technologies. Also, the quadratic dependence of frequencies on noises makes the CT decoherence an interesting physics problem. Thus we are motivated to study the decoherence of CTs. We consider noise from spin baths, which is one of the most relevant mechanisms of qubit decoherence. Various quantum many-body methods have been developed to study the decoherence of a central spin in spin baths. In particular, the cluster-correlation expansion (CCE) systematically accounts for the many-body correlations that cause the central spin decoherence. However, the CCE can not be straightforwardly applied to CTs in spin baths, for the expansion may fail to converge due to the effective long-range interactions resulting from the quadratic term of the noise (e.g., the second-order interaction mediated by hyperfine interactions for a nuclear spin bath). In this work, we develop a modified CCE method to tackle this class of decoherence problems. By diagonalizing the central spin Hamiltonian for each bath eigenstate of the hyperfine interaction, we find that the effects of long-range interactions are absorbed as fluctuations of central spin eigenenergies in the form of single-spin correlations. We apply the method to two specific systems, namely, nitrogen vacancy center electron spins in near zero magnetic field and singlet-triplet transition of two electrons in a double quantum dot. The numerical simulation shows that the modified CCE converges rapidly for the CTs.