The petal color of B. napus is usually yellow, but white, cream, golden yellow, orange, and other colors have also been reported. The pigmentation mechanisms and evolutionary processes of petal color in B. napus remain elusive. An analysis of the inheritance of the orange petal color (OPC) trait indicated that this trait was controlled by two recessive genes, termed Bnpc1 and Bnpc2. For fine mapping of the Bnpc1 gene, two backcrossing populations, BC4 and BC5, were developed from the cross between an OPC parent, X118, and a yellow petal color parent, R258. Whole-genome re-sequencing with bulked segregation analysis using BC4 individuals was conducted, and as a result, two major candidate intervals of Bnpc1 were identified on chromosome C09 of B. napus (C09: 1.000–5.464 and 6.491–7.777 Mb). Subsequently, the genetic and physical linkage maps were constructed for the BC5 population using 10 simple sequence repeat, two sequence-characterized amplified region and 12 insertion-deletion (InDel) markers. The Bnpc1 gene was located in scaffold_38 on C09 of B. napus and flanked by Indel-31 and Indel-5, with genetic distances of 0.083 and 0.042 cM, respectively. The interval distance between the two markers was 151 kb (4.624–4.775 Mb) and was included in the first re-sequenced candidate region (C09: 1.000–5.464 Mb). The present study may facilitate cloning of the Bnpc1 gene as well as marker-assisted selection for developing OPC B. napus varieties and revealing the mechanism of petal color formation in B. napus.