The design of metal hydroxide nanosheets on hollow carbonaceous nanostructures has attracted immense attention because of their unparalleled physical/chemical properties with sizeable intrinsic capability to load specific chemicals. Herein, a novel metal hydroxide based on hollow nitrogen-doped carbon nanoboxes shelled with a nanoporous copper hydroxide nanosheet (Cu(OH)2@N–C n-box) was fabricated. The structure of fabricated hollow nanomaterials was fully characterized by various physicochemical characterization techniques such as field emission scanning electron microscopy (FESEM), high-resolu1tion transmission electron microscopy (HRTEM), Brunauer–Emmett–Teller (BET) method, thermogravimetric analysis (TGA), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) and Raman spectroscopies, which confirmed that a complex core–shell structure with ordered two-dimensional Cu(OH)2 nanostructures on N–C n-box was successfully prepared. The Cu(OH)2@N–C n-box is used to fabricate an advanced electrochemical aptasensor to measure the protein enzyme trypsin. In addition, it acts as an excellent substrate with abundant functional groups and a large surface area for fixing and bonding aptamers on the modified glass-carbon surface. Each step of electrode surface modification was investigated through ferro/ferri cyanide probe signal changes. The designed aptasensor can determine trypsin in a linear concentration between 10 to 80 pg/mL and 10 to 80 ng/mL with a detection limit of 3 pg/mL. The proposed system also has a desirable selectivity in the presence of different interferences. This is the first report on the rational design of hollow carbonaceous materials hybridized Cu(OH)2 for the electrochemical application.