This study investigated how amylopectin (AP) chain-length distribution (CLD) influences the structural and functional properties of ten waxy rice varieties through a multiscale analysis. The fitting CLD parameters revealed that varieties such as YN12 and GMN2 contained the highest proportions of intermediate chains (h_iii~14.5~10.2) and long chains (h_v~0.552~0.477), resulting in higher gelatinization temperatures, including onset temperatures (T_o~60.2~66.4 °C), temperature peak (T_p~72.0~72.2 °C), and the conclusion temperatures (T_c~80.8~79.4 °C). Sample YN12 exhibited the lowest breakdown viscosity (BDV~748 cP), indicating higher thermal stability and stable pasting behavior. All of the samples showed relative crystallinity (Rc%) ranging from 19.3 to 22.8% with lamellar spacing of 8.8~9.4 nm. Sample YN12 exhibited the lowest enzymatic digestion rate (k~1.48 × 10⁻² min⁻¹) and the highest resistant starch (C_res~9.81%), reflecting restricted enzyme accessibility. In contrast, sample SN9714 and ZN106, characterized by a higher proportion of shorter branches in the long-chain region of AP CLD (β_vi~3.75~2.53), exhibited greater BDV (1407 cP) and faster digestion kinetics (k~1.90 × 10⁻² min⁻¹). The Rc% (22.83%) of NGXN was positively correlated with gelatinization enthalpy (ΔH~14.8 J/g). These findings highlight the pivotal role of AP CLDs in determining the structural, thermal, pasting, and digestive properties of waxy rice starch, offering molecular-level guidance for the development of rice-based ingredients with tailored functional characteristics.