Precipitate free zones (PFZs) near grain boundaries generally soften alloys. The quenching rate after solution treatment is an important factor influencing the width of PFZs in Al-Mg-Si-Cu alloy. This study explored the effects of high quenching rates on the grain boundary microstructures and mechanical properties of an Al-Mg-Si-Cu alloy. Samples of various thickness were quenched in water at room temperature and in ethylene glycol at −40 °C, respectively. The results showed that the rapidly quenched samples at −40 °C exhibited better comprehensive mechanical properties than the water-quenched samples. Transmission electron microscopy studies revealed the rapidly quenched samples had wider PFZs, shorter intragranular precipitates, and larger grain boundary precipitates (GBPs) than water-quenched samples. It is proposed that when the quenching rate exceeds the critical cooling rate, e.g., in water quenching or rapid quenching, the formation of PFZs is controlled by the solute depletion mechanism rather than the vacancy depletion mechanism. The nucleation and growth of GBPs thus lead to the depletion of solute atoms, resulting in wider PFZs rather than thinner PFZs according to previous knowledge. This research provides valuable insights into the application of rapid quenching technology for modifying alloys’ microstructures and properties.