Incorporating hetero-metal-atom, e.g., titanium, into zeolite frameworks can enhance the catalytic activity and selectivity in oxidation reactions. However, the rational design of zeolites containing titanium at specific sites is difficult because the precise atomic structure during synthesis process remained unclear.Here, a titanosilicate with predictable titanium distribution was synthesized by mediating vacancies in a defective MSE-type zeolite precursor, based on a predesigned synthetic route including modification of vacancies followed by titanium insertion, where electron microscopy (EM) plays a key role at each step resolving the atomic structure. Point defects including vacancies in the precursor and titanium incorporated into the vacancy-related positions have been directly observed. The results provide insights into the role of point defects in zeolites towards the rational synthesis of zeolites with desired microscopic arrangement of catalytically active sites.