We report on the validation of a method based on Kelvin probe force microscopy (KPFM) able to measure the different phases and the relative work function of polymer blend heterojunctions at the nanoscale. The method does not necessitate complex ultra-high vacuum setup. The quantitative information that can be extracted from the topography and the Kelvin probe measurements is critically analysed. Surface voltage difference can be observed at the nanoscale on poly(3-hexyl-thiophene):[6,6]-phenyl-C61-butyric acid methyl ester (P3HT:PCBM) blends and dependence on the annealing condition and the regio-regularity of P3HT is observed.