DH and IF2 populations, consisting of 261 and 234 lines respectively, constructed using the German winter rapeseed cultivar ‘Express’ (female) and the Chinese semi-winter line ‘SWU07’ (male), were used to detect QTLs related to oleic acid, linoleic acid and linolenic acid contents in different years. A total of 71 QTLs were detected in DH population in four-year environment and 4 QTLs in IF2 population in two-year environment. After eliminating the overlapped QTLs detected in different years or different populations, totally 51 QTLs for the three traits were obtained, 15 QTLs of which were persistently detected in more than two years. These 51 QTLs were located on 13 linkage groups. Among them, 18 QTLs related to oleic acid content were located on A01, A02, A04, A05, A07, A09, and C01, respectively, explaining phenotypic variation ranging from 3.44% to 13.97%, 12 QTLs related to linoleic acid content were located on A02, A06, A09, C01, and C02, respectively, explaining phenotypic variation ranging from 3.84% to 19.51%, and 21 QTLs related to linolenic acid content were located on A01, A02, A03, A04, A05, A08, A09, C01, C02, C03, and C06, respectively, explaining phenotypic variation from 2.86% to 11.91%. These results provide more genetic information for the improvement of fatty acid quality in rapeseed breeding.