Controlling the segregation behavior of primary Si in the solidification process of hypereutectic Al-Si alloy is crucial for enhancing the design ability of the solidification structure. To explore the separation condition and morphological evolution of primary Si in detail, a series of experiments concerning the coupling effect of a temperature field and electromagnetic stirring on the segregation behavior of primary Si were carried out. Experimental results show that the temperature field and fluid flow in the melt are two key points for controlling the segregation behavior of primary Si. The establishment of a temperature gradient in the Al-Si melt is a precondition for realizing the separation of primary Si. On the basis of the temperature gradient, the electromagnetic stirring can further strengthen the separation effect for primary Si, forming a Si-rich layer with 65~70 wt.% Si content. The formation of the Si-rich layer is a continuous growth process of primary Si by absorbing Si atoms from Al-Si melt with the help of electromagnetic stirring. The separation technology for primary Si is proposed to realize the segregation control of primary Si, which not only broadens the application of Al-Si alloys in the functionally gradient composites but also provides a low-cost supply strategy of Si raw materials for the solar photovoltaic industry.