A series of alkoxy substituted dihydronaphthyl-based [60]fullerene bisadduct derivatives (Cn-NCBA, n = 1-6), with the alkoxy chain length from 1 to 6 carbon atoms, were synthesized as acceptors for polymer solar cells (PSCs), aiming to systematically investigate the effects of fullerene derivative structures on the photovoltaic properties of PSCs. Though the absorption spectra and electrochemical properties of Cn-NCBA are nearly same, the PSCs based on P3HT:Cn-NCBA showed different photovoltaic properties. The device based on P3HT:C3-NCBA blend demonstrated the highest power-conversion efficiency (PCE) of ca 4.1%, while those with shorter or longer alkoxy substituted dihydronaphthyl-based [60]fullerene bisadduct derivatives showed relatively lower PCE. C5-NCBA and C6-NCBA with longer alkoxy chain length showed relatively low electron mobilities, leading to relatively poor photovoltaic performance. More importantly, we found that the alkoxy chain length changes the hydrophobicity of Cn-NCBA and thus the interfacial interaction and miscibility with P3HT, which were analyzed by interfacial tension and atomic force microscopy (AFM) measurements. The hydrophobicity of Cn-NCBA increased with the increase of alkoxy chain length. A distinct phase separation for the P3HT:C1-NCBA blend film due to the large interfacial tension and poor miscibility between P3HT and C1-NCBA could be one reason for the low PCE of the C1-NCBA-based devices. C3-NCBA may provide the most appropriate combination of electron mobility and miscibility with P3HT to achieve optimal photovoltaic properties. The current study provides the molecular structure-device performance relationship, especially with respect to the alkoxy chain length of Cn-NCBA and their interfacial interactions with P3HT, and suggests a design rule for high performance fullerene bisadduct acceptors for PSC applications.