CdSe/CdS heterostructured nanocrystals with quasi-type-II band alignments provide an interesting platform for studying the photoluminescence (PL) blinking associated with their unique morphologies. By using simultaneous measurements of the PL intensity, lifetime, and polarization anisotropy, we reveal the role of the electron delocalization during the blinking of single CdSe/CdS dot-in-rods. We found that a significant change in the PL polarization anisotropy distinguishes between two kinds of charged excitons with different electron delocalizations. We report our observation of unique polarized PL blinking governed by the band alignments and the Coulomb interactions between the charges inside and outside the dot-in-rod.