Multifunctional polymer-based biomaterials, which combine degradability and shapememory capability, are promising candidate materials for biomedical implants. An example is a degradable multiblock copolymer (PDC), composed of poly(p-dioxanone) (PPDO) as hard and poly(ε-caprolactone) (PCL) as switching segments. PDC exhibits a unique linear mass loss during hydrolytic degradation, which can be tailored by the PPDO to PCL weight ratio, as well as an excellent thermally induced dual-shape effect. PDC can be synthesized by co-condensation of two oligomeric macrodiols (PCL-diol and PPDO-diol) using aliphatic diisocyanates as coupling agent. Here, we investigated whether different morphologies could be obtained for PDCs synthesized from identical oligomeric macrodiols (PCL-diol with M n = 2000 g·mol-1 and PPDO-diol with M n = 5300-5500 g·mol-1) with 2, 2(4), 4-trimethyl-hexamethylene diisocyanate (TMDI) and 1, 6-hexamethylene diisocyanate (HDI), respectively. More specifically, atomic force microscopy (AFM) was utilized for an investigation of the surface morphologies in solution casted PDC thin films in the temperature range from 20 °C to 60 °C. The results obtained in differential scanning calorimetry (DSC) and AFM demonstrated that different morphologies were obtained when TMDI (PDC-TMDI) or HDI (PDC-HDI) were used as linker. PCL related crystals in PDC-HDI were more heterogeneous and less ordered than those in PDCTMDI, while HDI resulted in a larger degree of crystallinity than TMDI. This research provides some new suggestions for choosing a suitable coupling agent to tailor the required morphologies and properties of SMPs with crystallizable switching segments.