Zeolites have unique pore structures of molecular dimensions and tunable compositions, making them ideal for shape selective catalysis and separation. However, targeted synthesis of zeolites with new pore structures and compositions remains a key challenge. Here, we propose an approach based on a unique 3D-3D topotactic transformation, which takes advantage of weak bonding in zeolites. This is inspired by the structure transformation of PST-5, a new aluminophosphate molecular sieve, to PST-6 by calcination. The structure of nano-sized PST-5 crystals is determined by 3D electron diffraction. We find that the 3D-3D topotactic transformation involves two types of building units where penta- or hexa-coordinated Al is present. We apply this approach to several other zeolite systems and predict a series of new zeolite structures that would be synthetically feasible. This method provides a concept for the synthesis of targeted zeolites, especially those which may not be feasible by conventional methods.