Waxy, low-amylose and high-amylose rice starches were chosen to separate inner blocklets and outer shell from their granules under incomplete gelatinization. Isolated outer shells and swollen or merged inner blocklets, based on morphological structure of broken granules, were used as a probe to study the mechanism of differences between outer and inner blocklets formation, through molecular characteristics and starch granule-associated proteins (SGAPs) analyses. On the basis of molecular composition, it was concluded that shorter branched-chain amylopectin and some amylose chains were involved in the formation of inner blocklets (shells). While the stronger interaction occurred among outer blocklets (shell), those are composed of longer branched-chains amylopectin and few amylose molecules. SGAPs types and content of inner shells (blocklets) were higher than outer shell (blocklets). SGAPs not only interacted with amylose chains but also with amylopectin chains. The enzymatic machinery for biosynthesis, such as starch branching enzyme, plays a critical role in blocklet architecture.