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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 (<i>d4r</i>) 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 <i>d4r</i> 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⁻@<i>d4r</i> in pure silica zeolites ITQ-12. The F⁻@<i>d4r</i> species is thermal stable up to 300 °C. ITQ-12 with F⁻@<i>d4r</i> shows substantial catalytic activity in Biginelli reaction. Furthermore, the catalytic performance is proved to be positive correlated with the presence of F⁻@<i>d4r</i>, indicating the mild acid catalytic property of F⁻@<i>d4r</i>.