A series of biodegradable polyester copolymer (BPC)/organically modified layered zinc phenylphosphonate (m-PPZn) nanocomposites were successfully synthesized by polycondensation reaction and solution-mixed processing. The crystallization behavior and microstructure of BPC/m-PPZn nanocomposite are studied by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), and transmission electron microscopy (TEM). The WAXD and TEM data illustrate that most of the m-PPZn layered materials are partially intercalated or exfoliated in the BPC matrix. Lipase from Pseudomonas sp. as the enzyme was used for the enzymatic degradation tests. The increasing loading of m-PPZn enhances the weight loss of nanocomposite, suggesting that the existence of m-PPZn enhances the degradation of the biodegradable polyester copolymers.