Herein, we have presented a new insight for the synthesis of a hybrid heterogeneous catalyst. For this purpose, phosphonic acid tagged carbon quantum dots of CQDs-N(CH2PO3H2)2 encapsulated and assembled in channels of SBA-15 using a post-modifcation strategy. The mesoporous catalyst of functionalized carbon quantum dots (CQDs) was characterized by several techniques. CQDs-N(CH2PO3H2)2/SBA-15 as an excellent catalyst was applied for the preparation of novel pyrazolo[4′,3′:5,6]pyrido[2,3-d]pyrimidine derivatives by using pyrazole, barbituric acid and indole moieties at 100 °C under the solvent-free condition. The present work shows that a signifcant increase in the catalytic activity can be achieved by a rational design of mesoporous SBA-15 modifed with CQDs for the synthesis of biological active candidates. The synthesized compounds did not convert to their corresponding pyridines via an anomeric-based oxidation mechanism.