There is a lack of consensus on the crystal structure and polymorphism of Cu(I)-TCNQ even though an enormous work and great achievements have been reported for decades. This motivated us to perform a crystal structure prediction study [by using the Fast and Flexible CrystAl Structure Predictor (FFCASP)] combined with total energy calculations at the dispersion-corrected density functional theory (DFT-D) level. The ensemble of the optimized structures falls in two distinct regions based on the energy-density phase space. Our predictions located the thermodynamic phase (as a global minimum) and a conformationally similar local minimum structure to the experimentally proposed phase I, in the low- and high-density regions, respectively. The Rietveld refinement of the P2(1)2(1)2 local minimum structure to the experimental X-ray diffraction (XRD) pattern resulted in a structure with a density between the two regions. This polymorph, the kinetic product, becomes a high-energy local minimum structure after the full geometry optimization, being 35.03 kJ/mol above the global minimum. In addition, we found that the transition from the high- to the low-density region occurs via square planar coordination of copper atoms.