Few studies have reported on the continuous evolution of dual-linker zeolitic imidazolate frameworks' (ZIFs) structure and morphology during the crystal growth process. Herein, we report the synthesis of a novel ZIF material with CHA topology (ZIF-301-eIm) via the combination of a small-sized 2-ethylimidazole (eIm) with the large-sized 5-chlorobenzimidazole ligand. A series of derivative materials with distinct structures and morphologies were obtained via two pathways: (1) insufficient amount of eIm with prolonged crystallization time (pathway A) and (2) sufficient amount of eIm with prolonged crystallization time (pathway B). Various characterization techniques revealed the continuous evolution of structure and morphology during the crystal growth process. Insufficient amount of eIm and crystallization time (crystallization pathway A) led to ZIF-301-eIm derivatives with defective and open structures alongside an aggregated morphology of nanoparticles. Prolonging the crystallization time allowed small-sized eIm ligands to gradually fill into the framework, resulting in the formation of ZIF-301-eIm-A5 characterized by complete but dense structures with a perfect polyhedral morphology. Remarkably, a sufficient amount of eIm during synthesis (crystallization pathway B) formed ZIF-301-eIm-B1 with a similar structure and morphology to ZIF-301-eIm-A5 in just 1 day. ZIF-301-eIm-B3, with intact, dense structures, exhibits superior acetone/butanol separation performance compared to ZIF-301-eIm-A3 due to small pore windows and large cages facilitating selective adsorption of acetone through exclusion separation.