In this work, we have investigated two aniline based squaraine molecules, DBSQ(OH)2 and DHSQ(OH)2, for their potential application in organic photovoltaics. These two squaraine molecules are only different in side chain length (i.e. butyl vs. hexyl). Yet, their solar cell properties are drastically different (PCE = 3.6% vs. 1.9%). We have further investigated the reason behind the superior performance of DBSQ(OH)2 in absorbance spectra, hole mobility characterization and transmission electron microscopy. The results show that DBSQ(OH)2 has a higher hole mobility (5.1×10-4 cm2/V•s vs. 1.4×10-4 cm2/V•s) and is able to mix well with the fullerene acceptor compared to DHSQ(OH)2. Our work shows clearly that the long solubilizing alkyl side chain might be detrimental for OPV performance and that shorter side chains with enough solubility have great value when designing small molecules.