Flower color is an important trait in Brassica oleracea which can attract and guide the insect pollinators, protect flower organs, maintain the energy homeostasis in flower, reveal the rate and purity of out-crossing and indicate the introgressions of traits. In order to identify the genetic loci and candidate genes controlling flower color in B. oleracea, we constructed an F2 population from the cross between a B. alboglabra line (white flower) and a wild B. oleracea accession (yellow flower), and conducted QTL analysis using a previous molecular-marker-based genetic linkage map and a SNP microarray. By using a previously developed genetic linkage map, four QTL for flower color were detected from chromosome C02 and C03, respectively. The QTL on C03 was identified as a major QTL (explaining 78% of the phenotypic variation) with a partial dominant effect, and the QTL on C02 was a minor QTL (explaining 8% of the phenotypic variation) with an additive effect. To confirm and delimit the QTL, a QTL-seq analysis was conducted by using the B. napus 60K SNP microarray among 63 white and 31 yellow F2 genotypes. A significant peak was detected from 48.08 to 48.92Mb (0.84 Mb interval) on chromosome C03, within the confidence interval of the C03-QTL. One candidate gene BoCCD4 which is homologous to a known gene controlling flower color in B. napus was found from this QTL region. Nearly no expression of BoCCD4 was found by QT-PCR in yellow-flower B. oleracea genotypes, while high expression was detected in white-flower genotypes. A 3-bp insertion was detected at 778-780 bp of the coding region of BoCCD4 between two parental lines, and an indel marker LJ04 was developed accordingly, exhibiting co-segregation with flower color in 133 F2 genotypes of B. oleracea and 101 DH lines of B. napus (derived from B. alboglabra with white-flower). Our results suggest that the white flower in B. oleracea is controlled by a partial dominant locus on chromosome C03 and possibly regulated by a minor additive QTL on C02. Furthermore, the 3-bp insertion in the candidate gene BoCCD4 was assumed to result in the loss of function of BoCCD4, leading to a yellow flower. Thus, this study identified a novel allele of the candidate gene controlling the flower color in B. oleracea, and this result might contribute to understand the variation and evolution of flower color in Brassica species.