Sequence variations of starch synthesis-related genes (SSRGs) in rice (Oryza sativa L.) could result in starch component changes and eating quality differences. In this study, we investigated sequence variations of 10 SSRGs directly involved in starch biosynthesis in 104 rice accessions from a Heuristic core set using PCR- and -sequencing, including 4 ADP-glucose pyrophosphorylase (AGPase) large units, 2 AGPase small units, granule-bound starch synthase I (OsGBSSI), pullulanase 3 (PUL3), soluble starch synthase IIa (SSSIIaChr6) and another putative SSSIIaChr7. A total of 86 SNPs were detected from 9 of the 10 SSRG amplicons, leaving AGPL1 with no detectable SNP. The sequenced length ranged from 377 (OsAGPS2) to 834 bp (OsPUL3). In detail, 25 and 61 SNP loci were found to be present in the intron and exon parts of 9 amplicons, of which 41 loci were supposed to result in amino acid changes. Model-based structure analysis and kinship coefficients were evaluated based on previous 170 genome-wide SSR genotyping data. The subsequent association analysis revealed 11 associations between amylose content plus RVA data and 5 variations, of which the one between amylose content and a SNP from OsAGPS1 gene explained up to 16.25% of the phenotype variances. These SNP loci and association analysis could be employed to assist molecular breeding and help improve the rice quality.