The magnetic properties of π-conjugated bis (8-hydroxyquinoline) manganese (Mnq2) crystals are investigated. Rod-shaped Mnq2 crystals are prepared by using the physical vapor deposition method. Field emission scanning electronic microscopy spectra show that the Mnq2 nanorods have perfect plane quadrangular ends. Energy dispersive spectrometer and X-ray photoelectron spectroscopy analysis demonstrates that the powders and nanorods are the same compound with a high purity. X-ray diffraction analysis shows the high crystal quality of the prepared Mnq2 nanorods. The magnetic measurement, using alternating gradient magnetometer and magnetic property measurement system superconducting quantum interference device vibrating sample magnetometer, indicates that the prepared Mnq2 nanorods show a paramagnetic property at room temperature. First-principles density functional theory (DFT) calculations are used to study the electronic structure and magnetic properties of the prepared Mnq2 crystals. DFT calculations show that the magnetic moment of the Mnq2 isolated molecule is 5 μB, which mainly comes from the localized Mn 3d orbital. The energy difference between the antiferromagnetic and ferromagnetic states of the Mnq2 monoclinic cell is only 0.1 meV, which may explain the paramagnetic property observed in the prepared Mnq2 nanorods and also indicates the difficulty of preparing intrinsic ferromagnetic Mnq2 crystals.