Rapeseed oil is consumed worldwide, and its quality is closely related to the raw rapeseed material. In this work, the quality and flavor differences of rapeseed oil from twelve varieties with two growth periods were studied. The results showed that different varieties responded differently to changes in growth periods, with the GXY1 variety having the greatest combined effect. Shortening the growth period may reduce the moisture and protein content and increase the oil content of rapeseed. It may also enhance the oleic acid content and decrease the linoleic acid content. A total of 62 aroma compounds were identified by gas chromatography-ion migration spectrometry (GC-IMS), with aldehydes being the main flavor compounds. The flavor fingerprint of rapeseed oil derived from different varieties was effectively constructed. Seven key aroma compounds with relative odor activity value (ROAV) > 1 were identified, which significantly influenced the flavor of rapeseed oil. This work may provide new insights for selecting favorable rapeseed varieties for industrial production of high-quality rapeseed oil.