The results of a study of the influence of the system dimension on the generation and charge carrier transfer in copper phthalocyanine (CuPc) nanostructures are presented. It is shown that the observed broadening of the B and Q bands and the bathochromic shift of the maxima in the absorption spectra are due to the formation of the η-CuPc, α-CuPc, and β-CuPc phases in the CuPc nanostructures. The observed increase in short-circuit current and negative magnetic effect in CuPc nanostructures is associated with size effects.