Organic-inorganic hybrid perovskites have attracted considerable attention for developing novel optoelectronic devices owing to their excellent photo responses. However, conventional nanolithography of hybrid perovskites remains a challenge because they undergo severe damage in standard lithographic solvents, which prohibits device miniaturization and integration. In this study, a novel transparent stencil nanolithography (tSL) technique is developed based on focused ion beam (FIB)assisted polyethylene terephtha late (PET) direct patterning. The proposed tSL enables ultrahigh lithography resolution down to 100 nm and accurate stencil mask alignment. Moreover, the stencil mask can be reused more than ten times, which is costeffective for device fabrication. By applying this lithographic technique to hybrid perovskites, a highperformance 2D hybrid perovskite heterostructure photodetector is fabricated. The responsivity and detectivity of the proposed heterostructure photodetector can reach up to 28.3 A W −1 and 1.5 × 10 13 Jones, respectively. This tSL nanolithography technique based on FIBassisted PET direct patterning can effectively support the miniaturization and integration of hybridperovskitebased electronic devices.