Primordial black hole (PBH) is a fascinating candidate for the origin of binary merger events observed by LIGO-Virgo collaboration. The spatial distribution of PBHs at formation is an important feature to estimate the merger rate. We investigate the clustering of PBHs formed by Affleck-Dine (AD) baryogenesis, where dense baryon bubbles collapse to form PBHs. We found that formed PBHs show a strong clustering due to the stochastic dynamics of the AD field. Including the clustering, we evaluate the merger rate and isocurvature perturbations of PBHs, which show significant deviations from those without clustering.