Owing to their excellent thermal and chemical stability properties, low cost, and easy purification processes, metal phthalocyanines have received extensive research attention. To reveal the influence of alkyl-chain length of substituents on phthalocyanines rings, we prepared three small organic molecules based on copper phthalocyanine rings substituted with end-capping ethyl, butyl, and hexyl, alkyl groups. The molecular orientation and intermolecular pi-pi stacking of these materials were affected by the alkyl chains, resulting in different hole mobilities. The crystallization of the phthalocyanines improved as the carbon chain length was extended, which we attributed to increased intermolecular pi-pi stacking. We used density functional theory calculations and solution cyclic voltammetry and ionization potential measurements to confirm a small difference in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels. The morphology, molecular orientation and pi-stacking were affected by the introduction of alkyl chains and resulted in differences in the photovoltaic performance of solution processed PSC based on these copper phthalocyanines. The long-term stability of devices based on CuEtPc, CuBuPc, and CuHePc was improved by elongating the carbon chains because of the better hydrophobicity of the phthalocyanines.