A novel core-shell composite based on UiO-66-NH2@COF has been successfully prepared by covalent coupling and used as a platform for constructing ultrasensitive electrochemical aptasensors. This work establishes a new platform for biosensing using the MOF@COF composite to accurately and rapidly detect analyte for food safety and biological monitoring. Display omitted •The UiO-66-NH2@COF composite is successfully fabricated by a covalent linking approach.•This composite-based electrochemical aptasensor exhibits excellent electrochemical detection performance for ATP and CAP.•This aptasensor can precisely monitor analytes in various real samples. Exploration and construction of novel porous core-shell composites is of crucial significance due to their prospectively enhanced performances and far-ranging applications. Herein, microporous UiO-66-NH2 as a MOF core is coated by a mesoporous TAPB-DMTP−COF shell to construct the UiO-66-NH2@COF composite via a covalent linking approach. Importantly, the composite with retentive crystallinity and hierarchical porosity significantly improves the electrochemical detection performance, for instance ATP and antibiotic, because this composite has the high affinity between the phosphate groups of aptamers and dense Zr(IV) sites, and strong π-π stacking interaction between aptamers and this MOF@COF. The synthetic strategy in this systematic research expands a rational design for other MOF@COF core-shell hybrid materials to expand their promising applications.