In this study, two conjugated polyelectrolytes, polythiophene derivative (PTP) and poly[(9,9-bis [, , -trimethylammonium] hexyl)-fluorenylene-phenylene] dibromide (PFP), are utilized to modify the surface properties of ZnO electron extraction layer (EEL) in the inverted polymer solar cells (PSCs). Both higher short-circuit current densities and larger open-circuit voltages were observed from the inverted PSCs with ZnO/PFP or ZnO/PTP as compared with those only with ZnO EEL. The protonation process for PTP and PFP in solution is distinguished. Overall, more than 40% enhanced power conversion efficiency (PCE) from the inverted PSCs with ZnO/PFP, in which the PFP could be fully ionized in deionized water, and more than 30% enhanced PCE from the inverted PSCs with ZnO/PTP, as the case that the PTP could not be fully ionized in deionized water, as compared with the inverted PSCs with ZnO EEL were observed, respectively. These results demonstrate that the conjugated polyelectrolytes play an important role in enhancement of device performance of inverted PSCs and that the protonation process of the conjugated polyelectrolytes is critical to the modification for EEL in PSCs.