Neck-panicle is the only channel for assimilation substance that transports to the panicle. In this study， 122 chromosome segment substitution lines（ CSSL） derived from the cross between indica rice variety 93- 11 and japonica rice variety Nipponbare were used to investigate vascular bundle-related traits of neck-panicle and yield traits. The results showed significant correlation between vascular bundle-related traits of neck-panicle and yield traits. A total of 42 quantitative trait loci（ QTL） of vascular bundle-related traits and 45 QTL of yield traits were detected. Among them， 16 and 14 chromosomal regions with positive allelic effects were from Nippnbare and 93-11， respectively. Gained from the QTL mapping results of these two types of traits， six QTL clusters that regulate both vascular bundle-related and yield traits have been identified. Based on previous studies and the candidate gene analysis， two pleiotropic genes Ghd7 at the 9 Mb site of chromosome 7 and IPA1 at the 25 Mb site of chromosome 8 might be candidate， respectively. These results suggested a diversified genetic basis with partial common genetic mechanism for both rice vascular bundle-related traits and yield traits. Exploration of additional QTLs controlling“flow” and multiple genes regulating the interaction between“flow” and“sink” might provide theoretical and practical significance in rice breeding.