Poly(epsilon-caprolactone) (PCL) was filled with a very small amount of starch nanocrystals (SNC), with the objective being to control its crystallization. Three kinds of SNC particles, including a pristine one and ones acetylated with low- and middle-level substitutions, were used. Their roles during PCL crystallization were studied. The results reveal that pristine SNC acts as the nucleating agent, evidently increasing crystallization temperature and spherulite growth rate. However, nucleation activity of SNC particles reduces with their increasing level of surface acetylation. The middle-level-acetylated SNC particles even act as the antinucleation agent, impeding nucleation and subsequent spherulite growth of PCL. The phase affinity in those systems was then evaluated by the interaction energy parameter, aiming at a better understanding of the mechanism of role alterations of SNC particles. This work provides an interesting way to control PCL crystallization and opens a new door to extend applications of SNC particles.