Abstract A novel ab initio methodology based on high‐throughput simulations has permitted designing unique biselective organic structure‐directing agents (OSDAs) that allow the efficient synthesis of CHA/AEI zeolite intergrowth materials with controlled phase compositions. Distinctive local crystallographic ordering of the CHA/AEI intergrowths was revealed at the nanoscale level using integrated differential phase contrast scanning transmission electron microscopy (iDPC STEM). These novel CHA/AEI materials have been tested for the selective catalytic reduction (SCR) of NOx, presenting an outstanding catalytic performance and hydrothermal stability, even surpassing the performance of the well‐established commercial CHA‐type catalyst. This methodology opens the possibility for synthetizing new zeolite intergrowths with more complex structures and unique catalytic properties.