In this study, we identified a transcription factor, BnaC04.bZIP16, which belongs to the G subfamily of the bZIP family, that negatively regulates the accumulation of fatty acid in B. napus. BnaC04.bZIP16 directly binds to the promoters of BnaA08.OLEOSIN1 and BnaC03.PDH-E1 BETA to regulate seed fatty acid content. Furthermore, BnaC04.bZIP16 can be phosphorylated by the BnaA06.SnRK2. BnaA06.SnRK2-dependent phosphorylation can weaken BnaC04.bZIP16 protein stability as well as the DNA-binding ability. Interesting, overexpression of BnaA06.SnRK2 can significantly promote the accumulation of fatty acid. Our study identified a new function of BnaC04.bZIP16 in regulating the accumulation of fatty acids in B. napus and added it to the G subfamily of the bZIP family. Furthermore, our study proposed a regulatory pathway, “BnaA06.SnRK2-BnaC04.bZIP16-BnaA08.OLEOSIN1/BnaC03.PDH-E1 BETA” which provides novel insight into fatty acid biosynthesis.