Solar grade silicon (SOG-Si) and hypereutectic Al-Si alloys with low silicon (silicon composition below 25 pct) can be successfully obtained by separation of hypereutectic Al-Si alloy with high silicon (silicon composition above 30 pct) under an alternating electromagnetic field after post-processing. To explore the separation mechanism in detail, experiments were conducted in this study using a high-frequency induction furnace with different pulling conditions of the crucible which is loaded with Al-45 wt pct Si melt. Results demonstrate that the separation of hypereutectic Al-Si alloy is feasible through either a pull-up or drop-down process. The height of each separation interface between the compact and sparse parts of the primary silicon decrease as the pull-up distance rose. When the pulling rate is very low, resultant morphologies of compact primary silicon are rounded and polygonal, allowing for more effective separation of the primary silicon. A novel physical model is presented here based on the experimental results and simulation. The model can be used to effectively describe the separation mechanism of primary silicon from hypereutectic Al-Si melts under alternating electromagnetic fields.