  We study the clustering of primordial black holes (PBHs) and axion
miniclusters produced in the model proposed to explain the LIGO/Virgo events or
the seeds of the supermassive black holes (SMBHs) in arXiv:2006.13137. It is
found that this model predicts large isocurvature perturbations due to the
clustering of PBHs and axion miniclusters, from which we obtain stringent
constraints on the model parameters. Specifically, for the axion decay constant
$f_a=10^{16}~\mathrm{GeV}$, which potentially accounts for the seeds of the
SMBHs, the PBH fraction in dark matter should be $f_\mathrm{PBH}\lesssim7\times
10^{-10}$. Assuming that the mass of PBHs increases by more than a factor of
$\mathcal{O}(10)$ due to accretion, this is consistent with the observed
abundance of SMBHs. On the other hand, for $f_a=10^{17}~\mathrm{GeV}$ required
to produce PBHs of masses detected in the LIGO/Virgo, the PBH fraction should
be $f_\mathrm{PBH}\lesssim6\times 10^{-8}$, which may be too small to explain
the LIGO/Virgo events, although there is a significant uncertainty in
calculating the merger rate in the presence of clustering.
