Manganese phthalocyanine (MnPc) nanostructures with different morphologies were prepared on porous anodic alumina oxide (AAO) at different substrate temperature (Ts=50℃, 80℃, 120℃, 180℃, 240℃) in an organic molecular beam deposition (OMBD) system. The nanostructures morphologies were studied using scanning electron microscopy (SEM) and the results showed that the nanostructures morphologies could be modulated by the control of Ts, as a result, the continuous film was obtained at 50℃, whereas the nanorods (NRs), nanoribbons (NBs), nanowires (NWs), nanosheets (NSs) and nanoparticles (NPs) were facilely generated as Ts increased. At the same time, the density and the uniformity of the nanostructures decreased. The results of X-ray diffraction (XRD) indicated that only the β-phase polymorph formed throughout the growth process irrelevant to the Ts. Additionally, the ultraviolet visible (UV–Vis) absorption spectra demonstrated that the main absorption bands of MnPc nanostructures showed a remarkable band broadening as the Ts was increased.