We demonstrate the effective use of a magnetic field to improve molecular alignment, and the resulting enhancement of the electrical conductivity of organic molecular nanowires. The structures of phthalocyanine nanowires, which are produced in porous alumina templates, are characterized by X-ray diffraction. Careful analyses reveal that the crystal morphologies of the phthalocyanine nanowires, e.g., domain size, columnar alignment and face-to-face spacing, are improved by using a 12 T magnetic field. This is because of the anisotropic magnetic susceptibility of the π-conjugated phthalocyanine macrocycle. Electrical measurements of individual nanowires performed with a multi-probe scanning electron microscope show that such highly ordered molecular packing results in a seventeen-fold increase in conductivity.