Bivariate flow cytometry (FC) sorting with forward scatter (FSC) and side scatter (SSC) is a recently established novel technique to separate starch granules. However, the forming mechanism of starch FC-dependent popula-tion patterns (i.e. the number of subgroups (NS) and FSC/SSC-dependent distribution patterns) remain partly elusive. For this, the correlation of granular size and multi-scale structure of native starches and FC-dependent population patterns was investigated through employing a wide range of native starches originating from different species involving cereal-, pulse-, and tuber crops. Results showed NS was pertinent with particle size, amylose content (AC), amylopectin chains length distribution, lamellar structure, short-range ordered structure. The distinct NS was determined by impacts of native starch FSC / SSC-dependent distribution patterns. Specif-ically, starch granular size significantly correlated with both FSC and SSC-dependent distribution patterns. The proportion of chains with DP 6-12 was the intra-molecular decisive factor to influence short-range ordered structure, finally leading to FSC-dependent distribution patterns. By contrast, AC was another intra-molecular index to determine SSC-dependent distribution patterns through affecting lamellar structure and short-range ordered structure.