Rapeseed is one of the important oil crops in China, and the change of the composition in fatty acid content can affect the value of oil for edible and industrial use. QTLs linked to main fatty acid composition can be used for marker-assisted selection in fatty acid composition improvement in rapeseed. A segregation population BC1F1, derivered from a cross between a low erucic acid content line APL01 and a high erucic acid content variety M083 in Brassica napus L., was used to construct a genetic map and identify QTLs linked to main fatty acid composition in rapeseed. The genetic map containing 19 linkage groups was constructed with 251 markers of RAPD, SSR, and SRAP in rapeseed. Via WinQTLCart scanning, five QTLs linked to palmitic acid (C16:0) content were identified, which were located on linkage groups N3, N8, N10, and N13.The main-effect QTLs qPA8-1 and qPA13 linked to palmatic acid content in rapeseed explained 11.31% and 14.47% of the palmitic acid content variation in segregation population BC1F1, respectively. Three QTLs linked to stearic acid (C18:0) content were identified, which were located on the linkage groups N1, N8, and N16. The main-effect QTL qST16 accounted for 12.22% of phenotypic variation. Two QTLs, qOL8 and qOL13, both the main-effect QTLs linked to oleic acid (C18:1) content, were located in the region of m11e37b–A0226Ba267 on linkage group N8 and m18e46–m20e25a on N13, and accounted for 11.73% and 27.14% of phenotypic variation, respectively. Three QTLs linked to linoleic acid (C18:2) content were identified, and the main-effect QTL qLI8-1 accounted for 13.25% of phenotypic variation. Three QTLs, qLN1, qLN8, and qLN11, linked to linolenic acid (C18:3) content were identified, but they had a rather small effects on C18:3, and could be regarded as minor-QTLs. Four QTLs linked to eicosenoic acid (C20:1) content, and three of them, qEI8-1, qEI8-2, and qEI13, were main-effect QTLs, accounting for 12.20%, 10.22%, and 11.14% of phenotypic variation, respectively. Two QTLs qER8 and qER13, both the main-effect QTLs linked to erucic acid (C22:1) content, were located in the region of m11e37b–A0226Ba267 on linkage group N8 and A0301Bb398–m18e46 on N13, accounting for 16.74% and 31.32% of phenotypic variation, respectively. The main-effect QTLs linked to fatty acid content, which were located in the region near marker m11e27b on linkage group N8 and m18e46 on linkage group N13, could be used in marker-assisted selection in fatty acid improvement in rapeseed.