A flexible and transparent triboelectric nanogenerator (FT-TENG) has great potential for application in self-powered biosensor systems, electronic skin and wearable electronic devices. However, improving the output performance with little damage to its optical properties is challenging. Herein, we have developed an FT-TENG that has a well-ordered nest-like porous polydimethylsiloxane (NP-PDMS) film and graphene transparent electrodes. The NP-PDMS film with ordered pores is fabricated by hydrochloric acid etching of 500 nm sized ZnO spheres made of aggregated nanoparticles, having a light transmittance of 81.8% and a water contact angle of 118.62°. The FT-TENG based on the NP-PDMS film with a porosity of 12%, gives a maximum output of 271 V and 7.8 μA, which are respectively, 3.7 and 2.1-fold of those of a TENG with a flat PDMS film. The peak output power reaches 0.39 mW with a load resistance of 9.01 MΩ. The dielectric constant and effective thickness of the NP-PDMS film and the capacitance and charge transfer of the FT-TENG are systematically investigated. This work provides a novel and effective method to enhance the performance of FT-TENGs with little damage to their optical properties.