Organic molecular assemblies that can conduct both electrons and protons are attractive materials, as they have important applications in organic electronics and fuel cells. Herein, two three-dimensional conducting framework organic salt (CFOS) single crystals with excellent electron and proton conductivity have been successfully synthesized by a simple drop-wise addition and crystallization method. The packing structure of CFOSs can be controlled through changing the central atom of building unit from a single carbon atom to a silicon atom, which in turn affects the electron and proton conductivity of CFOSs. Furthermore, the theoretical calculation results show that electron conduction occurs through the 3D super stacked π-conjugated network pathways whereas the proton conduction occurs via a novel combination of Grotthus and vehicular diffusion. The general design strategy and intuitive results in this work will provide practically useful insights in the preparation of new conducting framework organic salt single crystals with tuneable structures for specific applications.