Yellow seed coat color (SCC) is a valuable trait in Brassica napus, which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus. In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 (dominant gene of yellow seed coat color and improved seed oil content 1) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus, which has excellent potential for yellow SCC and high SOC rapeseed breeding.