Abstract: Seed thickness is a crucial determinant of grain size and an important factor influencing yield and quality in rice. Identifying major pleiotropic QTLs that regulate grain thickness, yield and quality traits, and then subsequently conducting precise genotype selection, are crucial approaches for the synergistic improvement of yield and quality in rice. In this study, a set of BILs population was constructed through hybridization and backcrossing between high-quality japonica rice variety Sasanishiki and high-yield indica rice variety Habataki, which was used as the experimental material to investigate the relationship between seed thickness and quality traits, meanwhile to identify major pleiotropic QTLs. The results showed that there were significant correlations between seed thickness, length-to-thickness ratio, width-to-thickness ratio and quality traits. Distinct differences in quality traits were evident among lines with varying seed thickness types. Notably, significant differences in brown rice rate and head rice rate were found between thin seed and those with medium or thick seed lines, while no significant differences were observed between medium seed and thick seed lines. Additionally, thin grains exhibited significantly lower values for eating cooked quality, appearance, texture and score compared to medium seed and thick seed lines. A total of 60 QTLs for seed thickness and quality traits were detected, 12 QTLs for seed thickness and 48 for quality traits. These QTLs were clustered on chromosomes 1, 2, 4, 7, 8, 9 and 10. In particular, the QTL clusters on the chromosome 7 interval RM7~RM1279 and on the chromosome 10 interval STS10.1~RM5689 demonstrated significant pleiotropic effects on seed thickness, milling quality, appearance quality and eating cooking quality. This study has preliminarily elucidated the effects of seed thickness on quality traits, and then identified two pleiotropic loci that regulate both grain thickness and quality traits, which can provide theoretical and data support for the breeding of rice varieties with long and thick grains.