Polyethylene (PE) films are treated using an atmospheric pressure plasma jet (APPJ) with He or He/O2 gas for different periods of time. The influence of gas type on the plasma polymer interactions is studied. The surface contact angle of the PE film can be effectively lowered to 58° after 20 s of He/O2 plasma treatment and then remains almost unchanged for longer treatment durations, while, for He plasma treatment, the film surface contact angle drops gradually to 47° when the time reaches 120 s. Atomic force microscopy (AFM) results show that the root mean square (RMS) roughness was significantly higher for the He/O2 plasma treated samples than for the He plasma treated counterparts, and the surface topography of the He/O2 plasma treated PE films displays evenly distributed dome-shaped small protuberances. Chemical composition analysis reveals that the He plasma treated samples have a higher oxygen content but a clearly lower percentage of COO than the comparable He/O2 treated samples, suggesting that differences exist in the mode of incorporating oxygen between the two gas condition plasma treatments. Electron spin resonance (ESR) results show that the free radical concentrations of the He plasma treated samples were clearly higher than those of the He/O2 plasma treated ones with other conditions unchanged.