Despite the extensive potential of zeolitic imidazolate framework (ZIF) membranes in gas separation, the development of continuous, oriented ZIF membranes onto a polymeric substrate remains a significant challenge. This is presumably due to weak adhesion, and insufficient heterogeneous nucleation sites on the polymer surface. Herein, a layer of horizontally aligned poly(sodium‐4‐styrene sulfonate)‐modified halloysite nanotubes (PSS‐HNTs) with ample nucleation sites was used for templated growth of vertically oriented Zn‐ZIF‐L layers. Then we successfully developed the first well‐intergrown membranes of Co‐ZIF‐L on Zn‐ZIF‐L layers via heteroepitaxial growth. The stepwise deposition was utilized for the control of ZIF films orientation to avoid random nucleation and twins overgrowth. The integration of preferred vertical orientation and optimized grain boundary structure endowed the Co/Zn‐ZIF‐L membranes with a remarkable gas separation performance (CO2 permeance: 244.9 GPU, and CO2/N2 selectivity: 17.8). Our methodology provides a useful guideline to design mixed‐component, vertically oriented ZIF‐L to improve gas separation performance.