Piezoelectric nanogenerators (PENGs) based on highly aligned poly(vinylidene fluoride-co-trifluoroethylene) [P(VDF-TrFE)] nanofibers and micropatterned three-dimensional (3D) interdigital electrodes with good flexibility and highly output performance are constructed. The optimal PENG with 3D interdigital electrodes could charge the commercial capacitor of 100 nF to 3.2 V under the pressure of 2 kPa at a frequency of 1.5 Hz, which is nearly 10-fold higher than that of PENG with flat interdigital electrodes. The enhanced performance is mainly attributed to micropatterned 3D interdigital electrodes that could simultaneously optimize output voltages and currents of PENGs. And maximum power density of the optimal PENG could reach as high as 8.75 μW/cm2, which is superior to some PENGs based on PVDF and its copolymers. In addition, the optimal PENG generates a voltage as high as 150 V during fingers pressure/release cycles, the outputs could light up 32 light-emitting diodes after direct-current rectification. The flexible PENG can also be used to harvest the biomechanical energy of human movements, such as fingers tapping, walking, and jumping. The designed 3D interdigital electrodes represent a novel strategy to improve the performance of PENGs based on aligned nanofibers. This kind of PENG shows potential as an energy harvester and effective self-powered nanogenerator to drive wearable devices.