Here, a simple, efficient, and rapid solid phase extraction-gas chromatography (SPE–GC) method was developed for the simultaneous analysis of free/combined phytosterols in rapeseed and their dynamic changes during microwave pretreatment and oil processing. First, by comparing different methods for extracting free/combined phytosterols from rapeseed and rapeseed cake, the Folch method was considered to be the optimal method and was selected in subsequent experiments. Subsequently, the extraction method was validated by determining the recoveries of standards (brassinosterol, campesterol, β-sitosterol and cholesteryl oleate) spiked in rapeseed and rapeseed oil samples, and the recoveries were in the range from 82.7% to 104.5% and 83.8% to 116.3%, respectively. The established method was applied to study the dynamic changes of the form and content of phytosterols in rapeseed and its products (rapeseed oil and cake) during rapeseed microwave pretreatment and the oil production process. Additionally, the results showed that more than 55% of the free/combined phytosterols in rapeseed were transferred to rapeseed oil during the oil processing, and this proportion will increase after microwave pretreatment of rapeseed. This work will provide analytical methods and data support for a comprehensive understanding of phytosterols in rapeseed and its products during oil processing.