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-7,7,8,8tetracyanoquinodimethane (F 4 TCNQ •− ) 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 F 4 TCNQ •− 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.