Ni-base catalysts are promising candidate for the hydrogenation of furfural (FAL) to high-value chemicals. However, slow intermediate desorption and low selectivity limit its implementation. Identifying the catalytic performance of each active sites is vital to design hydrogenation catalyst, and tuning the geometrical sites at molecule level in PtNi could lead to the modification of electronic structure, and thus the selective for the hydrogenation of FAL was modulated. Herein, PtNi hollow nanoframes (PtNi HNFs) with three dimensional (3D) molecular accessibility were synthesized, EDX results suggested that Ni was evenly distributed inside of the hollow nanoframes, whereas Pt was relatively concentrated at the edges. DFT calculation demonstrated that PtNi significant decrease the desorption energy of the intermediate. This strategy could not only enhance the desorption of intermediate to improve the catalytic performance, but also transfer the adsorption mode of FAL on catalyst surface to selective hydrogenation of FAL to FOL or THFA. The PtNi HNFs catalyst afforded excellent catalytic performance for selective hydrogenation of a broad range of biomass-derived platform chemicals under mild conditions, especially of FAL to furfuryl alcohol (FOL), in quantitative FOL yields (99%) with high TOF of 2.56 h−1. It is found that the superior performance of PtNi HNFs is attributed to its 3D hierarchical structure and synergistic electronic effects between Pt and Ni. Besides, the kinetic study demonstrated that the activation energy for hydrogenation of FAL was as low as 54.95 kJ mol−1.