Physcion is abundantly present in the traditional medicinal plant Polygonum cuspidatum and exhibits remarkable bioactivities in suppressing various cancers and enhancing plant disease resistance. However, the O-methyltransferases involved in physcion biosynthesis in plants remain largely unexplored. In this study, we identified a regioselective emodin O-methyltransferase, PcEOMT1, from P. cuspidatum. PcEOMT1 catalyzed the methylation of emodin at the C6-OH position to produce physcion and exhibited strict substrate specificity. Maximal enzymatic activity of PcEOMT1 was detected at 37 °C and pH 8.0, along with high pH stability. Transient overexpression of PcEOMT1 in P. cuspidatum leaves further confirmed its pivotal role in physcion biosynthesis in vivo. Besides, molecular docking combined with site-directed mutagenesis revealed that the catalytic dyad and residue R133 of PcEOMT1 are major contributors to its regioselectivity toward emodin. This study enriches the understanding of the physcion biosynthetic pathway in plants and provides new insights into the selectivity mechanism of O-methyltransferases.