The nano-morphology of the active layer of organic solar cells has been studied extensively, as well as its link with the open circuit voltage of the device. However, considerably less attention has been dedicated to the relation between the active layer nano-morphology and the device short circuit current density. In this paper we study the relation between variations in the characteristics of the Poly-(3-hexylthiophene-2,5-diyl) (P3HT) chains and the resultant solar cell short circuit current density. We show that the lattice constant between two lamellar structure of P3HT inside the P3HT:Phenyl C70 Butyric Acid Methyl Ester (PCBM) blend reduced as the PCBM percent in weight was reduced in the analyzed range. The presence of nano-domains, which can be related to the intensity of the peak, also affects the short circuit current density. In this study the optimum value of the percent in weight of PCBM, to obtain high short circuit current density was obtained for 1:0.5 ratio in the blend. The distance constant between the lamellar structure of P3HT for each blend made was directly extracted from the Bragg’s law in combination with the μ-XRD analysis. The results were correlated with the electrical characterization for each blend and we found that when decreases the distance between two lamellar structure of P3HT there is a better performance on photovoltaic devices.