Exogenous gibberellins (GAs) are widely applied to increase crop yields, with knowledge about the physiological functioning and biochemistry mechanisms of these phytohormones improving; however, information remains limited about the effect of GAs on seed filling. In this study, the siliques (containing the seeds) of oilseed rape (Brassica napus L.) were treated with GA3 at 3 stages of seed filling. We confirmed that GA3 regulates the deposition of storage reserves in developing seeds. The percentage of crude fat in the seeds increased during the early stage, but remained stable during the middle and late stages. In comparison, the percentage of total protein decreased during the early and middle stages, but significantly increased during the late stage. In addition, Q-PCR was employed to analyze the expression level of related genes in response to GA3. It was found that the expression of WRI and ABI3 transcription factors corresponded to crude fat content and total protein content, respectively. The expression of storage reserve related genes DGAT, MCAT, SUC2, and GPT was consistent with crude fat content, whereas the expression of Napin corresponded to total protein content. The results of this study indicate that exogenous GA3 has a different effect on storage reserve deposition in seed during different stages of seed filling, and the effect might be achieved via changing the expression of related genes.