The effect of different polyhedral oligomeric silsesquioxanes (POSS) structures on the crystallization behavior and dynamic mechanical properties of biodegradable poly(ethylene succinate) was investigated in this work. Two kinds of POSS molecules with different structures, i.e., trisilanolisobutyl-polyhedral oligomeric silsesquioxanes (tsib-POSS) with an open cage structure and octaisobutyl-polyhedral oligomeric silsesquioxanes (oibPOSS) with a close cage structure, were separately incorporated into PES matrix at the same low loading of 1 wt %. Both types of POSS dispersed finely in the matrix, with the size of tsib-POSS aggregates being smaller than that of oib-POSS aggregates, which was in agreement with the solubility parameter difference between the two types of POSS molecules and PES matrix. The crystallization processes of PES under different conditions were accelerated by both types of POSS; moreover, oib-POSS showed stronger acceleration effect than tsib-POSS probably due to the good lattice matching between PES and oib-POSS. The crystallization mechanism and crystal structure remained unchanged for PES in the composites, despite the type of POSS. Tsib-POSS remarkably increased the storage modulus of PES, while oib-POSS slightly decreased the storage modulus of PES.