Herein, we report the preparation of Mn-doped Ni-based metal–organic frameworks (Mn-MOF) with 3D hierarchical flower-like superstructures through solvothermal synthesis. The Mn-MOF was assembled with 2D black phosphorous nanosheets (BPNSs) to achieve novel 2D/3D BPNSs/Mn-MOF nanocomposites, followed by the direct coupling of methylene blue (MB)-labeled DNA aptamer on the interface of the nanocomposites-modified glassy carbon electrode (GCE). The aptamer/BPNSs/Mn-MOF/GCE platform was utilized for the capture and efficient detection of stress-induced phosphoprotein 1 (STIP1). Experimental results confirmed that Mn-doping-induced the hierarchical petal growth of the flower-like 3D MOF and its assembly with BPNSs. GCE surface modifications with various components were studied by measuring electrochemical curves. The morphologies, microstructures and spectra of products were characterized. The optimal conditions used for electrochemical measurements were assessed. A smart aptasensor was explored by the aptamer/BPNSs/Mn-MOF/GCE that had multiple attractive merits, including synergistic effects of components, porous superstructures of hierarchical flower-like 3D Mn-MOF and specific aptamer-target recognition. The merits endowed this aptasensor with selective and sensitive signal responses to STIP1 over interferences. This aptasensor enabled the efficient detection of STIP1 in a broad range of 2 × 10⁻³–1 × 10⁴ ng mL⁻¹, accompanied by a low limit of detection of 1 pg mL⁻¹. This aptasensor realized the successful determination of STIP1 in practical samples, exhibiting high reliability and practicability.