Self-assembled supramolecular structures based on polyion complex (PIC) formation between oppositely charged polymers are attracting much attention for developing drug delivery systems able to endure harsh in vivo environments. As controlling polymer complexation provides an opportunity for engineering the assemblies, an improved understanding of the PIC formation will allow constructing assemblies with enhanced structural and functional capabilities. Here, we focused on the influence of the mixing charge ratio between block aniomers and catiomers on the physicochemical characteristics and in vivo biological performance of the resulting PIC micelles (PIC/m). Our results showed that by changing the mixing charge ratio, the structural state of the core was altered despite the sizes of PIC/m remaining almost the same. These structural variations greatly affected the stability of the PIC/m in the bloodstream after intravenous injection and determined their biodistribution.