In this study, the size control of organic materials and its dependence on sodium storage are investigated. Poly(pyrrole-squaraine) (PPS), a polymer containing zwitterionic repeating units, was selected as a proof for demonstration. The growth control of PPS micro/nanospheres could facilely be achieved via an in situ one-step polymerization. We found that the smallest-sized PPS showed the best rate performance and cycling performance, and the shortest activation process. Moreover, the Na-ion diffusion coefficient did not strictly correlate to the particle size. These results prove that the smaller size and the shorter ionic diffusion length rather than the ionic diffusion coefficient of the material dominated the charge transfer and ionic diffusion, thereby enhancing the rate performance.