PEDOT:PSS is promising conducting polymer in terms of its application to transparent and flexible electronic device. Generally, PEDOT:PSS is polymerized by oxidative polymerization using sodium persulfate and iron(III)sulfate as oxidants. After polymerization, especially sodium ions remain in aqueous state. It cause PEDOT:PSS solution to decrease electrical properties and colloidal stability. In this study, we reduced sodium ions to about 20ppm by exchange reaction. Also, we figure out the influence of sodium ions on PEDOT:PSS nanoparticles which related to interaction between PEDOT and PSS chain. The conformational changes between PEDOT and PSS chain are investigated with XPS, UPS, Raman spectroscopy and AFM. Further, the effect of sodium ions on colloidal stability of PEDOT:PSS is analyzed by viscosity change. And we finally investigate that unremoved sodium ions in PEDOT:PSS solution have a considerable influence on its electrical property and colloidal stability of PEDOT:PSS.