We applied 3D-printed microwire-array (MWA) structure to boost the energy conversion efficiency of laser proton acceleration. The advanced nano-printing technique allows precise control on the spacing and geometrical size of 3D structures at 100-500 nm resolution. Under irradiation of high contrast laser pulse (15J, 35fs), the MWA target generates over 1.2×1012 protons (> 1MeV) with cut-off energies extending to 25MeV, corresponding to top-end of 8.7% energy conversion efficiency from femtosecond lasers. When comparing to flat foils the efficiency is enhanced by three times, while the cut-off energy is increased by 30-70% depending on their thicknesses. By precisely controlling the array period via 3D nano-printing, we found the dependence of proton energy/conversion-efficiency on the spacing of the MWA. The experimental trend is well reproduced by hydrodynamic and Particle-In-Cell simulations, which reveal for the first time the modulation of pre-plasma profile induced by laser diffraction within the fine structures. Optimal geometry for laser-proton acceleration is therefore strongly modified. Our work validates the use of 3D-printed micro-structures to produce high efficiency laser-driven particle sources and pointed out the new effect in optimizing the experimental conditions.