We investigate theoretically the quantum transport properties of a twisted bilayer copper phthalocyanine (CuPc) molecular device, in which the bottom-layer CuPc molecule is connected to V-shaped zigzag-edged graphene nanoribbon electrodes. Based on a non-equilibrium Green's function approach in combination with density-functional theory, we find that the twist angle effectively modulates the electron interaction between the bilayer CuPc molecules. HOMO (highest occupied molecular orbital)–LUMO (lowest unoccupied molecular orbital) gap, spin filtering efficiency (SFE) and spin-dependent conductance of the bilayer CuPc molecular device could be modulated by changing the twist angle. The conductance reaches its maximum when the twist angle θ is 0° while the largest SFE is achieved when θ = 60°. The twist angle-induced exotic transport phenomena can be well explained by analyzing the transmission spectra, molecular energy level spectra and scattering states of the twisted bilayer CuPc molecular device. The tunable conductance, HOMO–LUMO gap and spin filtering versus twist angle are helpful for predicting how a two-molecule system may behave with twist angle.