is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed crops, and . Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in crops remain unclear.We collected seeds from a pair of accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. -means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of . A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G/M cell cycle transition, and the transcription factor seemed to positively stimulate the expression of two genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of and its target genes , , and . In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in .This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.