Biodegradable plastics are attracting attention as a solution to the problems caused by plastic waste. Among biodegradable plastics, polylactide (PLA) and poly (butylene succinate) (PBS) are particularly noteworthy because of their excellent biodegradability. However, the drawbacks of their mechanical properties prompts the need to compound them to achieve the desired strength. The characteristics of the interface of the composite material determine the realization of its final performance. The study of the interface and microstructure of composites is essential for the development of products from degradable polymers. The morphology evolution and microcrystal structure of spin-casted fully biodegradable (PLA/PBS) blend films were investigated using atomic force microscopy (AFM)-based nanomechanical mapping. Results show that intact blend films present an obvious phase separation, where the PBS phase is uniformly dispersed in the PLA phase in the form of pores. Furthermore, the size and number of the PBS phase have a power exponential relationship and linear relationship with PBS loading, respectively. Intriguingly, after annealing at 80 °C for 30 min, the PLA phase formed an orderly petal-like microcrystalline structure centered on the PBS phase. Moreover, the microcrystalline morphology changed from a “daisy type” to a “sunflower type” with the increased size of the PBS phase. Since the size of the PBS phase is controllable, a new method for preparing microscopic patterns using fully biodegradable polymers is proposed.