<p>Graphdiyne represents an emerging nanofiller of mixed matrix membranes for high-performance alcohol recovery by pervaporation due to its unique alkyne-rich and porous framework and hydrophobicity. However, such membranes often encounter a persistent challenge of nanofiller agglomeration within the polymer matrix, which diminishes the efficacy of graphdiyne during alcohol recovery. This study proposes a multilevel dispersion strategy that synergistically combines <i>in situ</i> confined growth, ultrasonication, atomization, and rotational shearing throughout membrane preparation to mitigate particle aggregation. The particle agglomeration scale in the polydimethylsiloxane matrix can be effectively reduced from 660 nm of triphenylamine-based graphdiyne to about 291 nm compared to the general stirring-casting method. The mixed matrix membrane loaded with 2.5 wt % triphenylamine-based graphdiyne demonstrated a permeate flux of 2.35 kg·m⁻²·h⁻¹ alongside a separation factor of 11.31 for a 5 wt % ethanol/water solution. Compared to the stirring-casting method, these performances represent enhancements of 41% in permeate flux and 80% in separation factor. Furthermore, a 96 h-continuous pervaporation test indicated the robust stability of the membrane, underscoring the potential for industrial alcohol recovery.</p>