Enzymatic degradation behavior of a lamella of single crystals of poly(R)‐3‐hydroxybutyrate (P(3HB)) with an extracellular polyhydroxybutyrate (PHB) depolymerase purified from Alcaligenes faecalis T1 has been investigated by atomic force microscopy (AFM) in order to obtain further information for the chain packing state of P(3HB) in a lamellar single crystal. Two kinds of P(3HB) single crystals with different molecular weights, denoted respectively as H‐ and L‐P(3HB) for high and low molecular weights, respectively, were prepared. The enzymatic treatment was conducted for P(3HB) single crystals adsorbed on a surface of highly ordered pyrolytic graphite. The enzymatic degradation of both P(3HB) single crystals generates several crevices crosswise across the crystal at an early stage. Subsequently, the enzymatic degradation yields numbers of cracks lengthwise along the crystal. In addition to these common features, the interval between cracks crosswise across a lamella in H‐P(3HB) single crystal is longer than that in L‐P(3HB) single crystal, and each crack has V‐shaped and rectangular shaped morphology for H‐ and L‐P(3HB) single crystals, respectively. Based on these results, it is concluded that a lamella of P(3HB) single crystal has straight degradation pathways, that may correspond to a switchboard region, along the long axis of the crystal, independent of molecular weight of P(3HB) samples, and that a H‐P(3HB) single crystal has broader degradation pathways with longer intervals crosswise across the crystal than a L‐P(3HB) single crystal.