Optimized nanomorphology in organic thin active layers is crucial for good performance in organic solar cells. However, the relation between morphology and electronic properties at nanoscale remains not completely understood. Here, we study the effect of film thickness and temperature annealing on the ordering of poly(3-hexylthiophene) chains when the polymer is blended with a columnar liquid crystalline molecule. Electronic absorption, atomic force microscopy measurements, and Raman spectroscopy show that morphology and chain ordering of the blend depend on the film thickness. We highlight the benefit of using a liquid crystal in organic blends, opening the way to use simple processing methods for the fabrication of organic electronic devices.