Polymer solar cells (PSCs) with ZnO electron transporting layer has been widely studied because ZnO has superior electron transport capability and high light transmittivity. However, lots of defects existed in ZnO film fabricated with sol-gel method and vacuum sputtering deposition can greatly increase carrier recombination at the ZnO interface. Therefore, it is important to enhance the performance of PSCs to inhibit defects and improve contact quality of ZnO interface. The regioregular poly(3-hexylthiophene) (P3HT) and 6,6-phenyl C61-butyric acid methylester (PCBM) based inverted PSCs with ZnO electron transporting layer have been developed by using layered magnetron sputtered ZnO and/or ionic liquid functionalized carbon nanopartilces (ILCNs) modification. The power conversion efficiencies (PCEs) of PSCs with ZnO layer sputtered with Ar and Ar/O2 gas are 22% and 28%, respectively. PSCs modified with ILCNs or layered sputtered ZnO can respectively reach 34% and 31%, and further up to 38% using layered sputtered ZnO and ILCNs integrated modification. PSCs using modified ZnO layer show the vanishment of negative capacitive behavior, lowering reverse dark current and better diode characteristics. The results indicated that using layered sputtered ZnO or ILCNs, or both integrated modification can efficiently inhibit the defects of ZnO interface and improve contact quality ZnO/P3HT∶PCBM interface. However, this integrated modification method is a more efficient strategy to enhance ZnO layer electron transporting and extraction capabilities, and further improve PCEs of PSCs.