The distribution of counterions and dopants within electrically doped semicrystalline conjugated polymers, such as poly(3-hexylthiophene-2,5-diyl) (P3HT), plays a pivotal role in charge transport. The distribution of counterions in doped films of P3HT with controlled crystallinity was examined using polarized resonant soft X-ray scattering (P-RSoXS). The changes in scattering of doped P3HT films containing trifluoromethanesulfonimide (TFSI–) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ•–) as counterions to the charge carriers revealed distinct differences in their nanostructure. The scattering anisotropy of P-RSoXS from doped blends of P3HT was examined as a function of the soft X-ray absorption edge and found to vary systematically with the composition of crystalline and amorphous domains and by the identity of the counterion. A computational methodology was developed and used to simulate the soft X-ray scattering as a function of morphology and molecular orientation of the counterions. Modeling of the P-RSoXS at N and F K-edges was consistent with a structure where the conjugated plane of F4TCNQ•– aligns perpendicularly to that of the P3HT backbone in ordered domains. In contrast, TFSI– was distributed more uniformly between domains with no significant molecular alignment. The approach developed here demonstrates the capabilities of P-RSoXS in identifying orientation, structural, and compositional distributions within doped conjugated polymers using a computational workflow that is broadly extendable to other soft matter systems.