Tetracycline antibiotic (TC) residues, such as doxycycline (DOX), tetracycline (TET), oxytetracycline (OTC) and chlortetracycline (CTC), have aroused public concerns due to their negative impact on human health and the ecological system. Herein, a 3D hierarchical dual-metal–organic framework, an Al-MOF@Mo/Zn-MOF heterostructure, is developed via an internal extended growth method for exceptionally high performance detection of TCs. The modified organic ligands with intriguing functional groups (–NH₂) exhibit specific recognition toward TCs, which makes the fluorescence of Al-MOF@Mo/Zn-MOF efficiently quenched by TCs via the synergistic effect of H-bonding interaction enhancing the electron transfer from –NH₂ on organic ligands to –CO–/–OH of TCs and the intense absorption of TCs at the excitation energy of Al-MOF@Mo/Zn-MOF. Particularly, the pre-concentration effect, induced by (i) metal nodes in dual-metal–organic frameworks providing unsaturated sites to recognize/adsorb the N and O atoms of TC molecules and (ii) the hierarchical nanoarchitecture enhancing mass transfer and alleviating the diffusion barrier to increase the contact area of MOF/TCs, endows Al-MOF@Mo/Zn-MOF with superior sensitivity. The Al-MOF@Mo/Zn-MOF reveals excellent anti-interference performances and ultra-low limits of detection (LODs) of 0.56, 0.53, 0.58 and 0.86 nM for DOX, TET, OTC and CTC. These acquired LOD values are two orders of magnitude lower than that of pristine amino-functionalized Al-MOF and comparable or even superior to those of previous fluorescence-based sensors. Satisfactory recoveries of 87.07–116.44% and RSDs of 0.22–2.30% are achieved in the detection of TCs in real water and food samples. These excellent sensing properties together with the advantages of facile fabrication, satisfactory stability and feasibility render the 3D hierarchical Al-MOF@Mo/Zn-MOF heterostructure promising for ultrasensitive detection of TCs in practical applications.