The reason(s) for why a complete duplication of the left hemisphere Heschl’s gyrus (HG) has been observed in people with reading disability are unclear. This study was designed to replicate and advance understanding of the HG and phonological decoding association, as well as test competing hypotheses that this HG duplication association is specifically localized to the HG or could be due to co-occurring atypical development of other brain regions that support reading and language development. Participants were selected on the basis of having a duplicated left hemisphere HG (N = 96) or a single HG (N = 96) and matched according to age, sex, and research site in this multi-site study. Duplicated and single HG morphology specific templates were created to determine the extent to which HG sizes were related to phonological decoding within each HG morphology group. The duplicated HG group had significantly lower phonological decoding (F = 4.48, p = 0.04) but not verbal IQ (F = 1.39, p = 0.41) compared to the single HG group. In addition, larger HG were significantly associated with lower phonological decoding in the duplicated HG group, with effects driven by the size of the lateral HG after controlling for age, sex, research site, and handedness (ps < 0.05). Brain regions that exhibited structural covariance with HG did not clearly explain the HG and phonological decoding associations. Together, the results suggest that presence of a duplicated HG indicates some risk for lower phonological decoding ability compared to verbal IQ, but the reason(s) for this association remain unclear.