As a solid acid, zeolite has been widely used in many fields such as tail gas treatment, petrochemical engineering, and the fine chemical industry. F− has been widely used in the synthesis of pure silica or high silica zeolites. To balance the charge of organic structure directing agents (OSDA), F− is often found located at the center of the double-4-rings (d4r) of the as-made zeolites. During calcination, fluorine ion is removed with the OSDA. We screened a series of composition building units and found that d4r is capable to retain F− in zeolite structure. We introduce the F− back after the calcination to create an unprecedented type of acid site, i.e., F−@d4r in pure silica zeolites ITQ-12. The F−@d4r species is thermal stable up to 300 °C. ITQ-12 with F−@d4r shows substantial catalytic activity in Biginelli reaction. Furthermore, the catalytic performance is proved to be positive correlated with the presence of F−@d4r, indicating the mild acid catalytic property of F−@d4r.