Starch molecular structure, in terms of chain-length distribution (CLD) and molecular size, are important structural features regarding to “(starch) structure-property” relations for starch-based foods. In this study, amylopectin CLDs from fluorophore-assisted carbohydrate electrophoresis (FACE) are parameterized by a biosynthesis-based model, amylose CLDs and molecular sizes of amylose and amylopectin are measured by size-exclusion chromatography (SEC), and statistically meaningful relationships are established between starch CLDs, starch molecular size, and amylose content using rice starches with a wide range of amylose content. This shows that amylopectin molecular size is increased by increasing the proportion of short amylopectin chains with degree of polymerization (DP) 6–32 and decreasing the percentage of long amylopectin chains with DP 63–100. On the other hand, molecular sizes of both branched amylopectin and amylose molecules are negatively correlated with amylose content, suggesting that high-amylose rice tends to have smaller amylopectin and amylose molecular sizes. These relations are rationalized in terms of chain-length effects on the production of branched amylopectin and amylose molecules between different rice cultivars, which could provide new insights regarding to starch “structure-property” relations.