The invention relates to the technical field of electrochemical materials, in particular to a nanofiber-based flexible array structure electrode and a preparation method thereof. The nanofiber-based flexible array structure electrode is prepared from an inner layer spinning solution and an outer layer spinning solution through electrostatic spinning, carbonization, hydrothermal growth and electro-deposition, the inner layer spinning solution is prepared from polyacrylonitrile (PAN), purified terephthalic acid (PTA), acidized carbon nanotubes (AC-MWNTs) and a solvent, and the outer layer spinning solution is prepared from polyvinylpyrrolidone (PVP), inorganic zinc salt, PTA and a solvent. According to the preparation method of the nanofiber-based flexible array structure electrode, the flexibility of carbon fiber is improved, and ZnO can be directly added into a precursor in the coaxial spinning process, so that the outer surface of the carbon nanofiber is loaded with nano ZnO evenly and firmly, the seed crystal coating process is omitted, thus the method is simple, efficient, high in universality, low in cost and environmentally friendly, an obtained product integrates the flexiblecharacteristic and bimetallic pseudocapacitance performance, and can form an independent electrode.