Deuterium labeling of semi-crystalline polymers can dramatically affect their crystallization behaviors. However, the influence of different labeled positions in a partially deuterated polymer on its crystallization is still far from understood. Here, we synthesized a series of selectively deuterated poly(ε-caprolactones) (PCLs) through ring-opening polymerization of ε-caprolactone with controlled deuteration sites, including fully protiated (D0), fully deuterated (D10), tetra deuteration at the 3-and 7-caprolactone ring positions (D4) and hexa deuteration at the 4-, 5-, and 6-caprolactone ring positions (D6). All the PCLs showed a similar lamellar structure and parameters. Differential scanning calorimetry (DSC) analysis revealed that the equilibrium melting temperature T 0 m , melting temperature T m , crystallization temperature T c , and crystallization kinetics changed systemically with the deuterium content except for D4, which indicates that the presence of CD 2 moieties on either side of ester group in the polymer chain combined with isotopic inhomogeneity could influence the chain packing. The nonmonotonic trend of T m as a function of deuterium content could be attributed to the difference in a hydrogen-bond like intermolecular interaction between different PCLs. Partially deuterated PCLs (D4 and D6) showed an Avrami index near 2. After analyzing the parameters at the same supercooling temperature ΔT c , the existence of two crystallization regimes of PCLs were detected.