Hexadecylamine-modified zinc phenylphosphonate (m-PPZn) and biodegradable poly(butylene succinate-co-adipate) (PBSA) were melt mixed using a single-screw extruder. Experimental results of wide-angle X-ray diffraction (WAXD) and transmission electron microscopy revealed that the stacking layers of the m-PPZn were partially intercalated and partially exfoliated into the PBSA polymer matrix. The biodegradation rates of PBSA using lipase from Pseudomonas sp. increase as the contents of m-PPZn increase. The degree of crystallinity the lamellar thickness determined using WAXD and small-angle X-ray scattering data decrease as the loadings of m-PPZn increase. It is necessary to point out that the changes of degradation rate, the degree of crystallinity, and the lamellar thickness are almost linearly proportional to the loading of m-PPZn. This finding of composite materials with controllable degradation rate would provide an important information for the manufacturing PBSA nanocomposites used in biodegradable mulching films for agricultures.