A series of 3D neutral boron imidazolate frameworks (BIFs) with octahedral metal centers were synthesized based on the charge-balancing principle. Au-Pd nanoparticles (NPs) with a mean size of 2.12 nm were then successfully obtained and encapsulated in these BIF structures through the simultaneous reduction of Au3+/Pd3+ ions by B-H bonds of tridentate boron ligands. The very small sizes of these Au-Pd NPs are attributed to the pore confinement effect of BIFs. This work not only brings new methodology for the construction of neutral BIFs but also suggests a new strategy for loading smaller-sized bimetallic NPs into BIFs.