A copper-1,4-naphthalenedicarboxylic acid-based organic framework (Cu-NDCA MOF) with different morphologies was synthesized by solvothermal synthetic route via a simple protonation-deprotonation approach. The synthesized Cu-NDCA MOFs were analyzed by diverse microscopic and spectral techniques. The FE-SEM and TEM image results exhibited the flake-like (FL), partial anisotropic (PAT), and anisotropic (AT)-Cu-NDCA MOFs formation obtained at different pH (3.0, 7.0, and 9.0) of the reaction medium. The AT-Cu-NDCA MOF/GC electrode not only increases the electroactive surface area but also boosts the electron transfer rate reaction compared to other modified electrodes (PAT- and FL-Cu-NDCA MOFs/GCEs). Under the optimized conditions, the modified electrode (AT-Cu-NDCA MOF) exhibited a sharp oxidation peak (+ 0.46 V vs. Ag/AgCl) and higher current response for rutin. The electrode provides a wide linear range from 1 × 10-9 to 50 × 10-6 M, a low detection limit of 1.21 × 10-10 M, LOQ of 0.001 μM, and sensitivity of 0.149 μA μM-1 cm-2. The AT-Cu-NDCA MOF/GC electrode exhibited good stability (RSD = 3.52 ± 0.02% over 8 days of storage), and excellent reproducibility (RSD = 2.62 ± 0.02% (n = 3)). The modified electrode was applied to the determination of rutin in apple, orange, and lemon samples with good recoveries (99.79-99.91, 99.24-99.69, and 99.53-99.83, respectively). Graphical abstract Anisotropic structure of Cu-NDCA MOFs and its modification on glassy carbon electrode for ultra-sensitive determination of rutin in fruit samples.