Rapeseed is an important commercial crop in the world, which is used for animal fodder and human consumption. The varied insolation duration and intensity is one of the main reasons for effecting the seed yield and seed quality of Brassica napus (B. napus) in worldwide. In this study, a highly oil seed content rapeseed cultivar “Qingyou 3” was subjected to light supplementary trial at both vegetative growth period and the seed productive stage. Different light quantity conditions were stimulated by light-emitting diodes (LED), main plot factor was land condition under LED (Treatment) and without LED (Control) in natural condition. The size and thickness of leaves, photosynthesis efficiency, seed oil content of B. napus increased significantly after light supplementary. Eighteen cDNA libraries were constructed from leaf segments (30 days after transplanting, 30 DAT) and seed 30 and 40 days after pollination (DPA) for RNA transcriptome sequencing. It was found that genes encoding lipid transfer protein, phenylpropanoid biosynthesis and plant hormone signal transduction were enriched in differentially expressed genes. This study is aim to identify the differentially expressed genes and signaling pathways in the leaves and seed of B. napus at the vegetative and seed productive stages under different light quantity. All the results provide the knowledge for understanding sufficient light plays a critical role in promoting photosynthesis, and is the basis of material accumulation and yield formation.