As the properties of nanomaterials are strongly dependent on their size, shape and nanostructures, probing the relations between macro-properties and nanostructures is challenging for nanoscientists. Herein, we deliberately chose three types of Ni(OH)2 with hexagonal, truncated trigonal, and trigonal hourglass-like nanostructures, respectively, as the electrode modifier to demonstrate the correlation between the nanostructures and their electrocatalytic performance towards L-histidine. It was found that the hexagonal hourglass-like Ni(OH)2 sample had the best electrocatalytic activity, which can be understood by a cooperative mechanism: on one hand, the hexagonal sample possesses the largest specific surface area and the tidiest nanostructure, resulting in the most orderly packing on the electrode surface; on the other hand, its internal structure with the most stacking faults would generate a lot of unstable protons, leading to an enhanced electronic conductivity. The findings are important because they provide a clue for materials design and engineering to meet a specific requirement for electrocatalysis of L-histidine, possibly even for other biomolecules. In addition, the hexagonal Ni(OH)2-based biosensor shows excellent sensitivity and selectivity in the determination of L-histidine and offers a promising feature for the analytical application in real biological samples.