Abstract: The changes of rapeseed industry’s external development environment and the disadvantages of rapeseed temporary storage purchase policy offer the opportunity for the implementation of rapeseed target price system, which will have an impact on rapeseed industrial security through the risk transmission of rapeseed industry chain. However, as the result of the different target price levels, the system has different impacts on rapeseed industry under different circumstances of decoupling or cohesion between international and domestic rapeseed markets and between long-run and short-run. In addition, some detail problems, including the market competition among oil processing enterprises, the flowing of domestic financial subsidies to overseas, the uncertainty of price subsidies’ legal status, the constraints of WTO agreements, the divergence on differential subsidies accounting and others, will all affect the implementation of target price system. Therefore, only by accurately analyzing the problems in all steps on the basis of scientific and reasonable design of rapeseed target price can we make sure that the rapeseed target price system reform is on the right direction.